diff --git a/docs/tools/SamplesTsvToJson.md b/docs/tools/SamplesTsvToJson.md
index dc17f44568eb4e5252ec5aaa5a42cb90d6746294..84a33413e9d98bd110d02952aaa46a4891cf59e1 100644
--- a/docs/tools/SamplesTsvToJson.md
+++ b/docs/tools/SamplesTsvToJson.md
@@ -58,7 +58,7 @@ To get the above example out of the tool one should provide 2 TSV files as follo
----
-| samples | library | bam |
+| sample | library | bam |
| ------- | ------- | --------- |
|Sample_ID_1 |Lib_ID_1 |MyFirst.bam |
|Sample_ID_2 |Lib_ID_2 |MySecond.bam |
diff --git a/protected/biopet-gatk-extensions/pom.xml b/protected/biopet-gatk-extensions/pom.xml
index 2767e37a47c8c34841217c73a5e8f05b1333943b..7560fbe54364e42f059b114298134fa300726cd2 100644
--- a/protected/biopet-gatk-extensions/pom.xml
+++ b/protected/biopet-gatk-extensions/pom.xml
@@ -25,7 +25,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
index 4679a3f7ad5cb542820ca229a1aa64ec5800dd1f..277390751529e743644dce7a2d9396b8d10b1228 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {
}
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
index 5813287fcb014b0bea08226428125462a2363c73..203354565b98b05a36d8227859823ee721ae60ee 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {
scatterCount = config("scattercount", default = 0)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
index 6c24a8e80431b131e870d70c677408cea05689b8..fbe2317e93d83c2fa6d3da58a9224dc6ba15a803 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount", default = 1)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
index 9384c20c379beffa41ab89b259ec1570f9b45645..138067f1679f3adbeae3d3dc366ea3ecf6355df6 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class CombineGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineGVCFs with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
index 943f149926613be116a91ab57738540c89bbd447..b811327b9cb154277b3efb7487a1a2085ae4b9d4 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class CombineVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineVariants with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
index e6cfbbd98d20b73f37171c6133959bb065f2796b..5bd36585d1de2f62c50cb46cedacc8f3a9bcf16d 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {
annotation ++= config("annotation", default = Seq("FisherStrand", "QualByDepth", "ChromosomeCounts")).asStringList
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
index 7dbe56c31bc3072a390c79ef8ed9b608db9103b3..30c7f890ac877194478119c9ee5187f283da6718 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
index 97105fbfff1fc6dbaadfd769d81f5fbdf11c95fe..44a3eac6607a6165920ab4d4564c9777119a1ca9 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
index fc9e02b36a5bcf3d401ae660456505e7b682bdd5..554208c3af1d791c71d97a17087f02321657de8c 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
index 66c688ebdaf09ff4cf9aa5c1fa190d75bf09ebc5..a884e83781227ce2b39b3f98573c3d89f8129d1b 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
index f1f5631b8c1f248f4d452200671d370b097ac066..abb27c5fc34d73ab62ffae928e622d6cda64c4d9 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class SelectVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
index b98495a0e3958ae0eda6cc9ecdde02657859daa2..a135b70c12e3f1deebb718b4ca788a9d0ebd5dce 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.UnifiedGenotyper with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
index 9aadadf49331f93d9b42ff3a1d9b35b7e9ddaffe..b26549622f2ee5131538baf8cc2882416bf3ae33 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class VariantAnnotator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantAnnotator with GatkGeneral {
if (config.contains("scattercount")) scatterCount = config("scattercount")
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
index 13f5027a3f9546e58e9ee084ea5429511785331d..9329c394d15bc0428a1c11077896a5026876be91 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
override def beforeGraph() {
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
index 908d01a695a956cc49f345c0d12a8506dc4af390..11560ea25e216a49515b618f03bbb9604accc731 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
class VariantRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantRecalibrator with GatkGeneral {
diff --git a/protected/biopet-gatk-pipelines/pom.xml b/protected/biopet-gatk-pipelines/pom.xml
index f4c667b932d14449e6051594ac3a4b30f4b8a2b8..90fbbf942bfd68c1b25a21174c60341634c78c92 100644
--- a/protected/biopet-gatk-pipelines/pom.xml
+++ b/protected/biopet-gatk-pipelines/pom.xml
@@ -25,7 +25,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
index ac17efd3c676b9fe5ed34bb2342fdf234347fec9..ecf4ccf901f8339db7da75c499bfae17a657eb16 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
@@ -6,7 +6,7 @@
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
import org.broadinstitute.gatk.queue.QScript
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
index 47d0525a13447531024d6568f63d2dd7619d27f1..e489c4afdf4a30b8ca0b2a965242eae7811ad24c 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.gatk
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import org.broadinstitute.gatk.queue.QScript
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
index 9c6abbb01bcc830a0ba0cf2ce946d2dd778c26cf..2f54cbbc70bc7c2666ef9c043017603c0b1c4b9f 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
@@ -5,7 +5,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.gatk
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ GenotypeGVCFs, SelectVariants }
import org.broadinstitute.gatk.queue.QScript
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index 9cde0a1f89ae94aeadebac6c58a5ac3887188ad8..3707ec2751cd21c82193f65c47281d294a764778 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineGVCFs, CombineVariants }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, SamToFastq }
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
index 232502bc7e43c17af0c0aea5b8f7e67569a4683e..772aa6887d7a7e4983059f84ea3ac7b455880c4a 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
@@ -6,7 +6,7 @@
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ ApplyRecalibration, VariantAnnotator, VariantRecalibrator }
import org.broadinstitute.gatk.queue.QScript
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index abc05e06cf8836e4d30954c07ed58071b975134b..6b99ca1706a0280a88b881e74e11a644e5ef1ab2 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -7,12 +7,12 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
-import nl.lumc.sasc.biopet.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
+import nl.lumc.sasc.biopet.extensions.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
index 3ab885710ea89d177689640579924a3eb6b657e4..cf5aa84c5bf75623b78ab3ad696a3d75300bd7fb 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
@@ -6,7 +6,7 @@
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, ShivaVariantcallingTrait }
import org.broadinstitute.gatk.queue.QScript
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
index 5981fd56aa6f22fb508e593aa740b87a48e0e7aa..1878d86fd150af451ab46fb69234ccbb66b05ec2 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
@@ -6,7 +6,7 @@
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.gatk.broad.GenotypeGVCFs
import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
import org.broadinstitute.gatk.queue.QScript
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
index 634a3fb17945144093f26dbcd11427b65474f7b6..9395daa1da479d97d5b5bd822379be5085b67c6c 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
@@ -8,11 +8,11 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.gatk.broad._
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam }
-import nl.lumc.sasc.biopet.tools.VcfStats
+import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
index 1609f5c31bb4a6b648a9a5aa4bb5a7de531e4714..2c60207a82fae9da823eb02d7a860b5dd8be1834 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+++ b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
@@ -8,10 +8,10 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.gatk.broad.{ HaplotypeCaller, UnifiedGenotyper }
-import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, VcfStats }
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
diff --git a/protected/biopet-protected-package/pom.xml b/protected/biopet-protected-package/pom.xml
index 14412813473824abddd4afffc328329e1633a387..c5d31a083c6e328bae807e9c1001510689a25d67 100644
--- a/protected/biopet-protected-package/pom.xml
+++ b/protected/biopet-protected-package/pom.xml
@@ -24,13 +24,13 @@
<properties>
<sting.shade.phase>package</sting.shade.phase>
- <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutableProtected</app.main.class>
+ <app.main.class>nl.lumc.sasc.biopet.BiopetExecutableProtected</app.main.class>
</properties>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala b/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala
similarity index 86%
rename from protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
rename to protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala
index 7b22399d3c33f1c71883b30c5aaeb7150324b4f5..4e725bb0b1e2002a323cc22f38c86b53ca4f14af 100644
--- a/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
+++ b/protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala
@@ -3,7 +3,9 @@
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet
+
+import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
object BiopetExecutableProtected extends BiopetExecutable {
def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List(
diff --git a/public/bam2wig/pom.xml b/public/bam2wig/pom.xml
index 8c86c694416b60ab26cb9a403679d7d85db3acbc..4ee5fd2681e87e9a999c4cfad22413dbd67a0bab 100644
--- a/public/bam2wig/pom.xml
+++ b/public/bam2wig/pom.xml
@@ -37,7 +37,12 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
index 50c44889853bfc684d84bb1082cfca38e3fa14cb..451350227e5620ae612212eb341e0acae49ad958 100644
--- a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.bamtobigwig
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.WigToBigWig
import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
index 405fdbbb00f1bcbbeeb7286a7b2edfd6dbadb0e0..6e9d6f658042d9179bf868ace85e234135adf4fc 100644
--- a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.bamtobigwig
import java.io.{ File, PrintWriter }
import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/bammetrics/pom.xml b/public/bammetrics/pom.xml
index 36a61b47a3f046790fa0d461b6b210fc60cc1ace..00a9b094e48a83b83105ce348060d94743a4d75c 100644
--- a/public/bammetrics/pom.xml
+++ b/public/bammetrics/pom.xml
@@ -35,7 +35,12 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
index 19daa26e625d0445459f26e50a7f5e8918e191d9..e2ad934d400e15283a8e94c428171e3e777e2172 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
index 4967f648483b5fbd68d93387ca6f6c8bcf7402e3..2d871d2663f5c17e0a1ea66e3434d267c01104d8 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
index c6ea6f5db5084bc3644cd6dacd22728821b024be..aab83e541800b520b4b871689536aff6fba84d0c 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] %>
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp
index 6497546891055ccdc882cbf2be5b609a7c1ae229..fd7820273f6164034df2f97f8d8d871fb0647be4 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(java.io.File)
<%@ var summary: Summary %>
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
index 294b7ba010b36d9673848d91f13d46b376fdefaa..f1bae9632f6bb046360496b0bf924515b791f794 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
@@ -1,5 +1,5 @@
#import(nl.lumc.sasc.biopet.utils.IoUtils)
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(java.io.File)
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
index ddb6817dd9e8dc90345881517637cbac53fcea56..8aea9602a65fd2282e38909b170722151ac13603 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
@@ -1,5 +1,5 @@
#import(nl.lumc.sasc.biopet.utils.IoUtils)
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(java.io.File)
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
index c5534f78cbeec347dc6bcbdf71fbceb70bba2c02..45f8da529dbab9bcd5c9a7dd6d93fd730b87715b 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/bedtools_cov_stats.py b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/bedtools_cov_stats.py
rename to public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/bedtools_cov_stats.py
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
index a0af2ced54e981db95952165d5053ee575367237..9905a23cfdcb9ac10ba96b1bb2ed43b3686604b8 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index bd546b41f3e24f8b9ad3e74cc7d547eeede3778b..24b0a29b1a7ce265ea145f404203f614da550884 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -17,14 +17,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
-import nl.lumc.sasc.biopet.scripts.CoverageStats
-import nl.lumc.sasc.biopet.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
+import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import org.broadinstitute.gatk.queue.QScript
class BamMetrics(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
index 395eebf1a615b0b8a1e5fc3405bb294d8b680475..f4138e12ec607ecfdcc9538347c83fbe6c9d4d16 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
-import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
-import nl.lumc.sasc.biopet.extensions.rscript.{ StackedBarPlot, LinePlot }
+import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
+import nl.lumc.sasc.biopet.utils.rscript.{ StackedBarPlot, LinePlot }
class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
val builder = BammetricsReport
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
similarity index 91%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
rename to public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
index 1ca92e3c62fcfe34ac8b289cdc50a93c8fbb0829..212724776c3dad98a1c514d17d6c66623c169127 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
@@ -13,13 +13,13 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.scripts
+package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala b/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
index d457009d9f3384f6278fd7702ee71eea8924531d..7e97b4a78e1176b1603a7ae5aec10057c4bd0175 100644
--- a/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+++ b/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
@@ -18,12 +18,12 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
-import nl.lumc.sasc.biopet.scripts.CoverageStats
-import nl.lumc.sasc.biopet.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
+import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
diff --git a/public/basty/pom.xml b/public/basty/pom.xml
index 8680fe20f5b03a774399b8fcc69ff86f572796d4..4dd6e5ef31827ea51eb1fc1c6976404570a9cd19 100644
--- a/public/basty/pom.xml
+++ b/public/basty/pom.xml
@@ -42,7 +42,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index 54fa824fc898e6cde1bc8ee1fecdf5e7ad40a50e..8476d1bbc56270b2da0d1df6eae20e19a6886bcc 100644
--- a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -16,7 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.basty
import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
diff --git a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
index d931860744eff28c2e730071af614ab37a0dfb11..1990085cef63fc60c637e04bb17811a20b837f85 100644
--- a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
+++ b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
@@ -25,7 +25,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.MultiSampleQScript
import nl.lumc.sasc.biopet.extensions.{ Cat, Raxml, RunGubbins }
import nl.lumc.sasc.biopet.pipelines.shiva.{ Shiva, ShivaTrait }
-import nl.lumc.sasc.biopet.tools.BastyGenerateFasta
+import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
import nl.lumc.sasc.biopet.utils.ConfigUtils
trait BastyTrait extends MultiSampleQScript {
diff --git a/public/biopet-core/pom.xml b/public/biopet-core/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..1b38b9f501d68479a60e52d40418367dd44358b3
--- /dev/null
+++ b/public/biopet-core/pom.xml
@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <parent>
+ <artifactId>Biopet</artifactId>
+ <groupId>nl.lumc.sasc</groupId>
+ <version>0.5.0-SNAPSHOT</version>
+ <relativePath>../</relativePath>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+
+ <artifactId>BiopetCore</artifactId>
+ <packaging>jar</packaging>
+
+ <dependencies>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetUtils</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>1.9.5</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.10</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.broadinstitute.gatk</groupId>
+ <artifactId>gatk-queue</artifactId>
+ <version>3.4</version>
+ <exclusions>
+ <exclusion>
+ <groupId>org.broadinstitute.gatk</groupId>
+ <artifactId>gsalib</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+ <dependency>
+ <groupId>org.broadinstitute.gatk</groupId>
+ <artifactId>gatk-queue-extensions-public</artifactId>
+ <version>3.4</version>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatra.scalate</groupId>
+ <artifactId>scalate-core_2.10</artifactId>
+ <version>1.7.0</version>
+ </dependency>
+ </dependencies>
+
+</project>
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/log4j.properties b/public/biopet-core/src/main/resources/log4j.properties
similarity index 100%
rename from public/biopet-framework/src/main/resources/log4j.properties
rename to public/biopet-core/src/main/resources/log4j.properties
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/License.txt b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/License.txt
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
similarity index 95%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
index e3eaba475acffa68c38293624e09e436e8976f62..0dcb32c20659700440cef5f214a6d0f7e6e5a0c4 100644
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
+++ b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.ttf b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.ttf
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.ttf
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.ttf
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff2 b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff2
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff2
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/fonts/glyphicons-halflings-regular.woff2
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
similarity index 88%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
index 49e7a18980f7efe03e57b0b4af763e4d90e845ea..442958b2c5ca531b87d40dedde06b112e7f7bec4 100644
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
+++ b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
similarity index 99%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
index fe56a9907bb51a322d382f7f9d6a957479fe6c50..b706ac45804afd61411115fbd47ca93bfbaa1fb9 100644
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
+++ b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var indexPage: ReportPage %>
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
similarity index 95%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
index 530d217358475f76461b79fc1fea83aee2746fc2..b12db503c8217bacf150c52a0e8c32b9949a4f6b 100644
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
+++ b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
similarity index 89%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
index 4769c64c19ce843ea2c0f340fcd964e2e813f2d4..20f6945618a17055380a9289d082c1655939f872 100644
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
+++ b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotXY.R b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotXY.R
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R b/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R
rename to public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
diff --git a/public/biopet-framework/src/main/resources/org/broadinstitute/gatk/queue/util/queueJobReport.R b/public/biopet-core/src/main/resources/org/broadinstitute/gatk/queue/util/queueJobReport.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/org/broadinstitute/gatk/queue/util/queueJobReport.R
rename to public/biopet-core/src/main/resources/org/broadinstitute/gatk/queue/util/queueJobReport.R
diff --git a/public/biopet-framework/src/main/resources/picard/analysis/baseDistributionByCycle.R b/public/biopet-core/src/main/resources/picard/analysis/baseDistributionByCycle.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/picard/analysis/baseDistributionByCycle.R
rename to public/biopet-core/src/main/resources/picard/analysis/baseDistributionByCycle.R
diff --git a/public/biopet-framework/src/main/resources/picard/analysis/gcBias.R b/public/biopet-core/src/main/resources/picard/analysis/gcBias.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/picard/analysis/gcBias.R
rename to public/biopet-core/src/main/resources/picard/analysis/gcBias.R
diff --git a/public/biopet-framework/src/main/resources/picard/analysis/insertSizeHistogram.R b/public/biopet-core/src/main/resources/picard/analysis/insertSizeHistogram.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/picard/analysis/insertSizeHistogram.R
rename to public/biopet-core/src/main/resources/picard/analysis/insertSizeHistogram.R
diff --git a/public/biopet-framework/src/main/resources/picard/analysis/meanQualityByCycle.R b/public/biopet-core/src/main/resources/picard/analysis/meanQualityByCycle.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/picard/analysis/meanQualityByCycle.R
rename to public/biopet-core/src/main/resources/picard/analysis/meanQualityByCycle.R
diff --git a/public/biopet-framework/src/main/resources/picard/analysis/qualityScoreDistribution.R b/public/biopet-core/src/main/resources/picard/analysis/qualityScoreDistribution.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/picard/analysis/qualityScoreDistribution.R
rename to public/biopet-core/src/main/resources/picard/analysis/qualityScoreDistribution.R
diff --git a/public/biopet-framework/src/main/resources/picard/analysis/rnaSeqCoverage.R b/public/biopet-core/src/main/resources/picard/analysis/rnaSeqCoverage.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/picard/analysis/rnaSeqCoverage.R
rename to public/biopet-core/src/main/resources/picard/analysis/rnaSeqCoverage.R
diff --git a/public/biopet-framework/src/main/resources/picard/analysis/rrbsQc.R b/public/biopet-core/src/main/resources/picard/analysis/rrbsQc.R
similarity index 100%
rename from public/biopet-framework/src/main/resources/picard/analysis/rrbsQc.R
rename to public/biopet-core/src/main/resources/picard/analysis/rrbsQc.R
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index ea2731c787eb0359ec42ef105fa3ccefe97c5f44..6084bb7b6a3b45f5ca184fe4c2634d8888846c77 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -18,7 +18,8 @@ package nl.lumc.sasc.biopet.core
import java.io.{ File, FileInputStream }
import java.security.MessageDigest
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.Input
@@ -110,7 +111,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if (executableToCanonicalPath) executable = file.getCanonicalPath
else executable = file.getAbsolutePath
} else {
- BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
+ Logging.addError("executable: '" + executable + "' not found, please check config")
}
BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
BiopetCommandLineFunctionTrait.executableCache += executable -> executable
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
similarity index 78%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 8bcb354588c52400cc2c6677839e5970149be191..f35c07a0a4497fa4a36e0b34a1b640cf8f03364c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -17,8 +17,9 @@ package nl.lumc.sasc.biopet.core
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
+import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
@@ -83,11 +84,11 @@ trait BiopetQScript extends Configurable with GatkLogging {
if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
- else BiopetQScript.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
+ else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
reportClass.foreach(add(_))
- BiopetQScript.checkErrors()
+ Logging.checkErrors()
}
/** Get implemented from org.broadinstitute.gatk.queue.QScript */
@@ -102,28 +103,3 @@ trait BiopetQScript extends Configurable with GatkLogging {
add(function)
}
}
-
-object BiopetQScript extends Logging {
- private val errors: ListBuffer[Exception] = ListBuffer()
-
- def addError(error: String, debug: String = null): Unit = {
- val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
- errors.append(new Exception(msg))
- }
-
- protected def checkErrors(): Unit = {
- if (errors.nonEmpty) {
- logger.error("*************************")
- logger.error("Biopet found some errors:")
- if (logger.isDebugEnabled) {
- for (e <- errors) {
- logger.error(e.getMessage)
- logger.debug(e.getStackTrace.mkString("Stack trace:\n", "\n", "\n"))
- }
- } else {
- errors.map(_.getMessage).sorted.distinct.foreach(logger.error(_))
- }
- throw new IllegalStateException("Biopet found errors")
- }
- }
-}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index b449fa2f6abf98c3c31ce8cee8ac09c58b7c7a3b..d8756c7b91cd27b330b4697aab0d94c9f436c98a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -152,7 +152,7 @@ trait MultiSampleQScript extends SummaryQScript {
private var currentLib: Option[String] = None
/** Prefix full path with sample and library for jobs that's are created in current state */
- override protected[core] def configFullPath: List[String] = {
+ override def configFullPath: List[String] = {
val sample = currentSample match {
case Some(s) => "samples" :: s :: Nil
case _ => Nil
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
index 612a3753d3cf6d49a86e7c577bf51da0c5880948..dcede52573eb901026c7e62deb9d071d486df9fb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
@@ -17,8 +17,9 @@ package nl.lumc.sasc.biopet.core
import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
+import nl.lumc.sasc.biopet.utils.{ MainCommand, Logging }
import org.apache.log4j.{ PatternLayout, WriterAppender }
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
similarity index 94%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
index d3ae0023adada50480a9006a55c6f2cb8e5e346e..7a7013fd6dd8eecec23b33801894ef660fc22660 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
@@ -18,7 +18,8 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import htsjdk.samtools.reference.IndexedFastaSequenceFile
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
import scala.collection.JavaConversions._
@@ -99,7 +100,7 @@ trait Reference extends Configurable {
/** Check fasta file if file exist and index file are there */
def checkFasta(file: File): Unit = {
if (!Reference.checked.contains(file)) {
- if (!file.exists()) BiopetQScript.addError(s"Reference not found: $file, species: $referenceSpecies, name: $referenceName, configValue: " + config("reference_fasta"))
+ if (!file.exists()) Logging.addError(s"Reference not found: $file, species: $referenceSpecies, name: $referenceName, configValue: " + config("reference_fasta"))
if (dictRequired) Reference.requireDict(file)
if (faiRequired) Reference.requireFai(file)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
index 996a51ce0e04280d4fe49367cdda3793ce2e8b4a..a3317faf604a9ae80c02ad0c3d9751fbc65849b9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.core
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Argument
/**
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
new file mode 100644
index 0000000000000000000000000000000000000000..dcb50896014e5c6b96fc9940a74a0dacabc94bd8
--- /dev/null
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
@@ -0,0 +1,17 @@
+package nl.lumc.sasc.biopet.core
+
+import nl.lumc.sasc.biopet.FullVersion
+
+/**
+ * Created by pjvanthof on 11/09/15.
+ */
+trait ToolCommandFuntion extends BiopetJavaCommandLineFunction {
+ def toolObject: Object
+
+ override def getVersion = Some("Biopet " + FullVersion)
+
+ override def freezeFieldValues(): Unit = {
+ javaMainClass = toolObject.getClass.getName.takeWhile(_ != '$')
+ super.freezeFieldValues()
+ }
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
similarity index 95%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
index 8ad2a31cbf782f77f00dd1b7b0415d84bc264a2b..90e577e01804ac1884d71de9613e3416d837fc92 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
@@ -13,12 +13,12 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions
+package nl.lumc.sasc.biopet.core.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for md5sum */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
index 59e4ed04c39f66e88e2f02fc0fde9b954d3efa5e..044b43676cd66cc68bcaeb00ade521def63c62de 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions
+package nl.lumc.sasc.biopet.core.extensions
import java.io.{ File, FileOutputStream }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
similarity index 58%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
index 4566cd4f1b26f08f2af84e31735b6514dfd10d6a..c773de6155b5a771f242dbbe83a4a21f98089eaa 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/RscriptCommandLineFunction.scala
@@ -13,24 +13,27 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet.core.extensions
-import org.apache.log4j.Logger
+import java.io.{ File, FileOutputStream }
-/**
- * Trait to implement logger function on local class/object
- */
-trait Logging {
- /**
- *
- * @return Global biopet logger
- */
- def logger = Logging.logger
-}
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.rscript.Rscript
+
+import scala.sys.process._
/**
- * Logger object, has a global logger
+ * General rscript extension
+ *
+ * Created by wyleung on 17-2-15.
*/
-object Logging {
- val logger = Logger.getRootLogger
-}
\ No newline at end of file
+trait RscriptCommandLineFunction extends BiopetCommandLineFunction with Rscript {
+
+ executable = rscriptExecutable
+
+ override def beforeGraph(): Unit = {
+ checkScript(Some(jobTempDir))
+ }
+
+ def cmdLine: String = repeat(cmd)
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
index e52bb1f5a9074f779f74d643cc3238ed22443d38..6c1bc388153f37d746cbf8a173a5ecc85c7201d5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
@@ -16,10 +16,9 @@
package nl.lumc.sasc.biopet.core.report
import java.io._
-
-import nl.lumc.sasc.biopet.core.summary.Summary
-import nl.lumc.sasc.biopet.core.{ Logging, ToolCommand, ToolCommandFuntion }
-import nl.lumc.sasc.biopet.utils.IoUtils
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.summary.Summary
+import nl.lumc.sasc.biopet.utils.{ ToolCommand, Logging, IoUtils }
import org.broadinstitute.gatk.utils.commandline.Input
import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
import scala.collection.mutable
@@ -34,6 +33,8 @@ trait ReportBuilderExtension extends ToolCommandFuntion {
/** Report builder object */
val builder: ReportBuilder
+ def toolObject = builder
+
@Input(required = true)
var summaryFile: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summarizable.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index c59438133af902b84edf83b87a5e02e03f0dc58a..52c77fe8a63a090f2c4bb776da39647f9a35379e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.File
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.extensions.Md5sum
+import nl.lumc.sasc.biopet.core.extensions.Md5sum
import scala.collection.mutable
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index 0dad01e5bb8e46355f150fc406914b423391a72a..3db4607d6288f84b204033ee3db186ee76771935 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetCommandLineFunctionTrait, BiopetJavaCommandLineFunction, SampleLibraryTag }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.{ LastCommitHash, Version }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
index 2092ea7324cb62997debf195189169744de26281..a2c4b8c2507e95d83618fc54e3f238ccfa009769 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
@@ -50,7 +50,7 @@ import java.util
import java.util.ResourceBundle
import nl.lumc.sasc.biopet.FullVersion
-import nl.lumc.sasc.biopet.core.Logging
+import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.queue.engine.{ QGraph, QGraphSettings }
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging, ScalaCompoundArgumentTypeDescriptor, ClassFieldCache }
import org.broadinstitute.gatk.queue.{ QCommandPlugin, QScript, QScriptManager }
diff --git a/public/biopet-framework/src/test/resources/log4j.properties b/public/biopet-core/src/test/resources/log4j.properties
similarity index 100%
rename from public/biopet-framework/src/test/resources/log4j.properties
rename to public/biopet-core/src/test/resources/log4j.properties
diff --git a/public/biopet-extentsions/pom.xml b/public/biopet-extentsions/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..cb5afbe9b02186ef0cf213d1ebb46f29a4148de4
--- /dev/null
+++ b/public/biopet-extentsions/pom.xml
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <parent>
+ <artifactId>Biopet</artifactId>
+ <groupId>nl.lumc.sasc</groupId>
+ <version>0.5.0-SNAPSHOT</version>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+
+ <artifactId>BiopetExtensions</artifactId>
+
+ <dependencies>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetCore</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.10</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+</project>
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py b/public/biopet-extentsions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
similarity index 100%
rename from public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
rename to public/biopet-extentsions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
index 2429702c83aa40193f25be6e6fe0f4b8b05fb62e..321cb8b9c5960936da9d8f5bcac0d2fdb9937627 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Wrapper for the bgzip command */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index 088123a760b7cc9f14821a1a7f0d7aa37ed27d99..5a574b729fb7fa4c7b27c674845f069fd01cb4ca 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
index 7f2493d570f3575fc62b47e1850e5c4b15772a81..74901be9ca04722b54877032e0654d14d057ceb4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
index 64db7b8b7d85c6a66fe6088a793c8ec762d391cd..30a1ca0f418ac0e5f3495ef75ba7478a28f5adc7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
index 3f33b314852c0e0f6c1e1524395083a238df0a28..ffadc5d2dfc6fd8bbb4c22ea099d96be344b8cdf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
index 181b92c80d835ef2b33d92ea9afc3c4288004812..f6278426ee4f76c8b4cca1cc1a40863ce22b24eb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index 9e2838f21aa38c0a56ab87e3823a8ba9b83bc4dc..6f0eea34bde472b7be68ba275244681974776b64 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
index bf43610e42767b1c875f714c9f86470a58c1d161..0e7cc1077a5a14f6ce8f829f6fb9009bd8930e40 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
index ec3d03615ca8c6d6efa74e256d40beb7f7c2c348..8604639800a0bf93620c9fe790a1cbccd5b32874 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
index 8513e207342b7ea618406fe3f259074ef50bebe0..cdd44e6b2ba95ceff528ad4c136ade3c693cb03f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class Gzip(val root: Configurable) extends BiopetCommandLineFunction {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
index 829b86a7354ff4c120522a375e10776938c24e37..adf25ba3cf1caf2b159950c0457c85d2ac4c71f0 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
index 5ac1042920a97571e91511907d6dfc89271c0e4b..c066b976f21808e982900f9e8a78fcd651cfe8f6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
index 2b042e35e95bd6c83022142aac4f51a38e313dbf..9943886d53127eca520fbd351c9cc66f9f3bba58 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for pbzip2 */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
index 55f482701d13dfe44b9bfc5db11d62e8f39065c2..ae017f08881677cb60620f0f860c1dea2765ccee 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import scalaz.std.boolean.option
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index 0f86bf810791c5c3e5106ebab025f6938e7a3b88..53539ac9f9ae9ca46e3a7543e5375e690e916e6a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
index 9b21f0afade3e8915ca0717f9510560e9e575a3f..ecc4a52e5d167bb48967f091a356955b91f09975 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for sha1sum */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
index fffa435a7db5829da05b78736b62ca8d284b6be3..938d36e432f9162942980f0da99be084bf455fa8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
index 4db91af20df5293b400313f811904c40e8aff5b4..0ae011df060922f88fd22c22e20c45bdcee13801 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
index 6014b6399b4b35d4bceb49a9684fe7fd419555a1..84ec59eb9f5bc83b3c6e6b9980c4f29121a2d12d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
index 3aee7ba2f859fed7fdd2f990454da2b9cf7b5e40..4a80600c52cb602c579c5b09ba27931c09f2c338 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
index 708bfb0363a6d664370380695962717d55a3d6bf..98379193eec3008a2545bd2dc3001713b1df0083 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
index b124a08aa5944beebff8507c09646618c4bc0ab7..7a9efb0ff7087fcca7462dd6efc9d0ac7432f1b4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
index 34d5f899ea29599ac2a2ede30452593dc72f6c84..eaef86a39e2d02e22b49cb2a0a9a12073b841934 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
index 96da2a82483746f628fff42d2beea4a06673164d..974f5e9140be562da77bd4f167888b6945d9a70b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for zcat */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
index f79d0fb562e30cfc9ebeb533feb038d854f56caa..537cd377daa4c3f731541717e5378159a9f4cdc7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bcftools
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** This extension is based on bcftools 1.1-134 */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
index 04a1525d767e6665b776ff4c7e08910fa1eb9dec..98024e79e25aa0c98624e2ff0e01783d37e35537 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for bedtools coverage */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
index 6a7e7be7f0751f958f3d09d3c4d798f523fc100d..067a6a951b190a8fec019379a82ab7068d48aaeb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
index 2f01ca14d557493ad7bf22e9733ddb5171c5314d..75f179ad326939d65f01031a4e909c59565e4906 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for bedtools intersect */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
index 9ccf70fa9a4d0310e65a3933933ae0150e16763b..9f662e3d7830f542a7361c11c5803385afef44ac 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
import org.broadinstitute.gatk.queue.QScript
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
index 4b2efd150947d8d49c21f4ee526bc26bb0177fd0..a760c10b1be47f7e5414dee9a2cf7f7aa9e4a416 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
index 6a67b3714527683ecc94505693c566164b71d55d..2b310aaf8c6b38933f4c11badedfbf7d57084bef 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerConfig(val root: Configurable) extends BiopetCommandLineFunction {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
similarity index 92%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
index ce756711ac16e728f9c31a985eeb10c8623b330a..5174f66af523bf5fd3b84ade4d0cc49ce1903946 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
index de4dbe5d34752cc42199818a19a946e9fedf013f..b4f69dd845db9487f85a5258deaf618cb687de46 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index 9ba2f49c70676cc2287debfc62fc52f0f02e0a6e..31c65252872c4ac3c01493bbf4ddc8abb6f5456e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
index c6afc21d0e26953632758f054d0d37f349ee0ab1..46632e010dd8ffd66ec295201a2a1d25c315f76a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
index a2d979ca078257a4fb85f3d3591d89f6a49a74db..73ec165e16ad4f797ec5d2219c87d2a80b8f8697 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
index bb71bd5351231ec230c947d093e0adfd1ca4162c..02a0afec29287b3cda576842b36db9316ad0b401 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.clever
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction with Reference {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
similarity index 94%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
index 7d061ed819bc91c8d0fa641783ff89a50e58bd6f..1488cabc468071702f4b2c748e2a2363dac9d810 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.extensions.conifer
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
abstract class Conifer extends PythonCommandLineFunction {
override def subPath = "conifer" :: super.subPath
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
index d181d99b561c721b79f7f3b484d29aac07b58f93..284d0e059dea542f2550db22b086b4a4db9837da 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class ConiferAnalyze(val root: Configurable) extends Conifer {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
similarity index 95%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
index e016fedc00f509ddb3cc2bd05da1d96274f4054a..7450ed1d31b184b690ae31b8c5071da2747d3bb2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class ConiferCall(val root: Configurable) extends Conifer {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
index afc22bd865cb8ac2d0fc82044ce471158468ebad..abc690ccd5d09881d9daf2161be8ca1b406f6934 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class ConiferExport(val root: Configurable) extends Conifer {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
index ae4e1684e6f451ca7435a364227515cb7f67ac37..915b171d82cfba083cd7696ad487f5cebc1fe0ec 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class ConiferRPKM(val root: Configurable) extends Conifer {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
index bac2fd131d016155b023eb059f57c3bfc4c2c8d2..b5fabe35e56555ba1723ab9270c04578b6bde23e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.delly
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.Ln
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
index da8815abb930aaff02bd2939d08ca9d5c338f1e2..8863baa50114a0c33c8d4e1d3df5c07101168284 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.delly
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
index 1d2c90a5fae95869c89cd7caf8a49a83724884e1..2b4ebcc3866aad7fd2308f3b3d6755abadf5931b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
index cbca06001123644f490eb4fc598ab41151620194..7fff0430095b9ccc20123a71380eaff31c0e11c8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.igvtools
import java.io.{ File, FileNotFoundException }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
index da53b6841c64345420465d60edfd7d2a08fabeee..ae475e2ca9fe24775af0d017ca7df42e1905cd09 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
@@ -19,7 +19,7 @@ package nl.lumc.sasc.biopet.extensions.kraken
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for Kraken */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
index a07e315606a171eb5f3063d8fe900067b042cb61..01d0cb731e361c35c98ea515e2fbcb749025d4b4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
@@ -19,7 +19,7 @@ package nl.lumc.sasc.biopet.extensions.kraken
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for Kraken */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
index f96b9b80f452fead71e18598fcb871fe14a1c72b..10fb47713bff4ef480159bcfe4fe3eb787751d96 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.macs2
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for macs2*/
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
index 0df7dffef9fe020014e2395bc90a1f5002791ce6..f2f7a1031a0892dc47605822f3a8f0ad1a656fdf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard AddOrReplaceReadGroups */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
index 6562eb3483859e03d89783fef55d9d095919666c..99f42e2b6e99f04c40880a2437bec242a386d672 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
index ac69069e314999124488c18a4de7285c92c04d7b..23351a6459e283f4c5330e80a7a34918e6dd276a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
index 3a456cede39d40a886619b6c74788426b8e1e91d..7a02e7be2165472094085b1700f60d08d75b667c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index 167aeca9b5515c3001f242f10ea7e2637c5ba383..52ddd61758c50c27f7a3f8def6dc69f6815f4c9d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
index c5f4c5a8a91059efe094581bb77c262c61ccc269..b94b623c867019bf65d39987a796fa0808336b66 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
index dd420840fba426c3db051ea13dd777c1db638cdb..0ecc053022d3aaefdded69907d97618a891322d0 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
@@ -18,7 +18,8 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
@@ -74,7 +75,7 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
case p if p == Programs.CollectBaseDistributionByCycle.toString =>
outputFiles :+= new File(outputName + ".base_distribution_by_cycle_metrics")
outputFiles :+= new File(outputName + ".base_distribution_by_cycle.pdf")
- case p => BiopetQScript.addError("Program '" + p + "' does not exist for 'CollectMultipleMetrics'")
+ case p => Logging.addError("Program '" + p + "' does not exist for 'CollectMultipleMetrics'")
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
index 334741278863473708c1df29f858483d2db9c78c..112c6afe42bbe93275d8713d74c330dc93b4bd5f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
index 07f90c676b508f2324bae8c88c8053eeb1b57e67..537ed3eea0eebfd88980bd41a29358591077e96a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
index 0f05a37a0fb3808b01bccade7c13d969e30abef9..97b429e3ff9c702fbe06b5efb07b6557b4ee44c9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
index 5603024007ce18a4e979c31b1087e897820732d4..0a7acc94375dc2457419ea82bd0730ad3ea63846 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class GatherBamFiles(val root: Configurable) extends Picard {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
index 33c2a0be9a6b8e65eec264c49919983397924bc4..f7a77d20d459f8cbc8bfee32b12ece7e99d7a2eb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
index f347ad3574fc6b13ab2be8abb6bdb4b1f64057fb..d358ba4e6b0d78c60a4d67d07f337be82750ea6f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard MergeSamFiles */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index d5f3b2078b706a269e6ef4754ce35db447b39841..9d00e0608818e3e76ece3eb9bfc35464fe3e0754 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Logging }
-import nl.lumc.sasc.biopet.utils.tryToParseNumber
+import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.utils.{ Logging, tryToParseNumber }
import org.broadinstitute.gatk.utils.commandline.Argument
import scala.io.Source
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
index 2acc114d04e5384906692967031db604687a72bd..c52d15d42e7a338ab0cb879ecf595f92bbe561ad 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class ReorderSam(val root: Configurable) extends Picard with Reference {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
index 31445cf9ca1545318d77a4e021a9771d87fa15fb..6b26f48b8fafdcec9f79f39bd73d5c558f66f78f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard SamToFastq */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
index 918ad656168c537644bc9a30c1b288fcdf2e38df..078e794a5f14823e69b315c1f494efa4a1acc097 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/** Extension for picard SortSam */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
index c79ca9bd313015bd3ba845d9ed26abe134f2438a..e6ee2e0c1c369ea99f58a41bf273406d04fdbc33 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for sambemba flagstat */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
index 9100127039f55ea12b4e59fbf6b5b6d12216170b..7be1ce5272bead43f9300a63e05834355e998325 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for sambemba index */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
index 85dab9b244b46813dee407ee055a9b295f274a79..2f89774db35e5f9d6f22518aa2ff3588f70d053f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for sambemba markdup */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
index 7f3f567b30b908123da709861c36bb14e16da3fe..83464fa4972e6f1aa3b9f74733ff8589985e91d8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for sambemba merge */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
index ee1dca3bd4a32d7f7f7ad0c5d934e2186614b1d1..4a012d22950898d662c6285ddf47fbec06e6bce1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for sambamba flagstat */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
index 4a86970d6c93b05d0313f694f71e7b56469c7e22..2035cbdb6231b01fe611310928abbf2053e4d04e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for samtools flagstat */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
index efb851cca152a4fd76d1f7fa4502e774f47b4d66..449b49cf0fbc3e1620a804347ce3d61790210183 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
import java.io.File
import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for samtools mpileup */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
index f340dec710db4ad5297cb4ea8168e4896f44b97e..fca6e84ccd15bfd6af4c72723269e13afda7f13c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for samtools view */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
index 04dfce893586d731a7fb07adf2d86e13822824cd..157f5d6500317b52dcaed70220d9eed5fd2bde4b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.seqtk
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
index 0bfd114d9c7c22faad81cdd57232de6ff08a695e..773e466981ef703c8fc8f91b91b51b25b33d3054 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
+++ b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.varscan
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class Mpileup2cns(val root: Configurable) extends Varscan {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
diff --git a/public/biopet-extentsions/src/test/resources/log4j.properties b/public/biopet-extentsions/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/biopet-extentsions/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/biopet-framework/src/test/resources/picard.alignmentMetrics b/public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.alignmentMetrics
similarity index 100%
rename from public/biopet-framework/src/test/resources/picard.alignmentMetrics
rename to public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.alignmentMetrics
diff --git a/public/biopet-framework/src/test/resources/picard.dedup.metrics b/public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics
similarity index 100%
rename from public/biopet-framework/src/test/resources/picard.dedup.metrics
rename to public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics
diff --git a/public/biopet-framework/src/test/resources/picard.insertsizemetrics b/public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.insertsizemetrics
similarity index 100%
rename from public/biopet-framework/src/test/resources/picard.insertsizemetrics
rename to public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.insertsizemetrics
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
similarity index 97%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
index 1ffd257e0a53c23ce37812601e8b63464cc2dd37..7a5a541899981f9a3a6bf25396ea23d64afd60d3 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
+++ b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.extensions
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.SkipException
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
similarity index 92%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
index 49edf90b2eaf52f3c48757c060a705a9a72d2f77..48a6bade41d2fdd65faacceb40c6dc750cac841f 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
+++ b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
@@ -31,7 +31,7 @@ class CollectAlignmentSummaryMetricsTest extends TestNGSuite with Matchers {
@Test
def summaryData(): Unit = {
- val file = new File(Paths.get(getClass.getResource("/picard.alignmentMetrics").toURI).toString)
+ val file = new File(Paths.get(getClass.getResource("picard.alignmentMetrics").toURI).toString)
val job = new CollectAlignmentSummaryMetrics(null)
job.output = file
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
similarity index 92%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
index 52a0f2d3f39ad72151b9ff4d445aa609e82bbfc2..88f2b330f7e70d2da8f48c222408500d2cb83ea0 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
+++ b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
@@ -31,7 +31,7 @@ class CollectInsertSizeMetricsTest extends TestNGSuite with Matchers {
@Test
def summaryData(): Unit = {
- val file = new File(Paths.get(getClass.getResource("/picard.insertsizemetrics").toURI).toString)
+ val file = new File(Paths.get(getClass.getResource("picard.insertsizemetrics").toURI).toString)
val job = new CollectInsertSizeMetrics(null)
job.output = file
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
similarity index 92%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
index 9b6d9b575ea5d0a2a5a69cb77f2fa575926a2294..23cfcddc5f3ff58a15e867a853e760684794d4c9 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
+++ b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
@@ -31,7 +31,7 @@ class MarkDuplicatesTest extends TestNGSuite with Matchers {
@Test
def summaryData(): Unit = {
- val file = new File(Paths.get(getClass.getResource("/picard.dedup.metrics").toURI).toString)
+ val file = new File(Paths.get(getClass.getResource("picard.dedup.metrics").toURI).toString)
val job = new MarkDuplicates(null)
job.outputMetrics = file
diff --git a/public/biopet-framework/.gitignore b/public/biopet-framework/.gitignore
deleted file mode 100644
index a6f89c2da7a029afa02b6e7a2bf80ad34958a311..0000000000000000000000000000000000000000
--- a/public/biopet-framework/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/target/
\ No newline at end of file
diff --git a/public/biopet-framework/README.md b/public/biopet-framework/README.md
deleted file mode 100644
index 3dc04d5cb35ab582ccae7d07a8bf73abbb99db8b..0000000000000000000000000000000000000000
--- a/public/biopet-framework/README.md
+++ /dev/null
@@ -1,9 +0,0 @@
-Biopet Framework
-=======================
-Framework to build pipelines with
-
-
-License
-===
-
-A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL license; For commercial users or users who do not want to follow the AGPL license, please contact sasc@lumc.nl to purchase a separate license.
diff --git a/public/biopet-framework/examples/bam-metrics.json b/public/biopet-framework/examples/bam-metrics.json
deleted file mode 100644
index 87ee73e04005c5847e414b544e9179f02a742eab..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/bam-metrics.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
- "reference": "bla",
- "bedtools": { "exe": "test"},
- "samtools": { "exe": "test"},
- "targetBed": ["target_1", "target_2"]
-}
diff --git a/public/biopet-framework/examples/biopet-defaults.json b/public/biopet-framework/examples/biopet-defaults.json
deleted file mode 100644
index 1f505ce90551039e629943430b55cae644b30517..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/biopet-defaults.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
- "genotypegvcfs": { "scattercount": 100 },
- "variantannotator": { "scattercount": 10 },
- "realignertargetcreator": { "scattercount": 30 },
- "combinevariants": { "scattercount": 10 },
- "printreads_temp": { "scattercount": 30 },
- "indelrealigner": { "scattercount": 30 },
- "haplotypecaller": { "scattercount": 100 },
- "unifiedgenotyper": { "scattercount": 100 },
- "baserecalibrator": { "scattercount": 30 },
- "basty": {
- "haplotypecaller": { "scattercount": 20 },
- "unifiedgenotyper": { "scattercount": 1 },
- "multisample": { "unifiedgenotyper": { "scattercount": 100 } },
- "baserecalibrator": { "scattercount": 1 },
- "indelrealigner": { "scattercount": 1 },
- "printreads_temp": { "scattercount": 1 },
- "realignertargetcreator": { "scattercount": 1 },
- "genotypegvcfs": { "scattercount": 1 },
- "combinevariants": { "scattercount": 1 }
- }
-}
diff --git a/public/biopet-framework/examples/flexiprep.json b/public/biopet-framework/examples/flexiprep.json
deleted file mode 100644
index 177cfdd255b702361588cadd76215939d0ef6372..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/flexiprep.json
+++ /dev/null
@@ -1,8 +0,0 @@
-{
- "fastqc": { "exe": "/data/DIV5/SASC/common/programs/FastQC/fastqc_v0.11.2/fastqc" },
- "flexiprep": {
- "seqtk": {"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"},
- "cutadapt": {"exe":"/home/pjvan_thof/.local/bin/cutadapt"},
- "sickle": {"exe":"/data/DIV5/SASC/pjvan_thof/bin/sickle"}
- }
-}
diff --git a/public/biopet-framework/examples/gatk-benchmark-genotyping.json b/public/biopet-framework/examples/gatk-benchmark-genotyping.json
deleted file mode 100644
index 89d0d7d92a4cb8fc86a9d0c8d2995227cf7876b0..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/gatk-benchmark-genotyping.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
- "gvcffiles": ["test4.vcf", "test5.vcf"],
- "reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
- "dbsnp": "bla",
- "haplotypecaller": {
- "stand_call_conf": 20,
- "stand_emit_conf": 20
- }
-}
diff --git a/public/biopet-framework/examples/gatk-genotypeing.json b/public/biopet-framework/examples/gatk-genotypeing.json
deleted file mode 100644
index 083b938251d1ef0601736b9f1d02a60aa119bff3..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/gatk-genotypeing.json
+++ /dev/null
@@ -1,8 +0,0 @@
-{
- "reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
- "dbsnp": "bla",
- "haplotypecaller": {
- "stand_call_conf": 20,
- "stand_emit_conf": 20
- }
-}
diff --git a/public/biopet-framework/examples/gatk-pipeline.json b/public/biopet-framework/examples/gatk-pipeline.json
deleted file mode 100644
index b9b1ef2b6190bddedd5ae4c94570834ab4cb7fc5..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/gatk-pipeline.json
+++ /dev/null
@@ -1,40 +0,0 @@
-{
- "reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
- "reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
- "samtools": { "exe": "test"},
- "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
- "flexiprep": {
- "seqtk": {"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"},
- "cutadapt": {"exe":"/home/pjvan_thof/.local/bin/cutadapt"},
- "sickle": {"exe":"/data/DIV5/SASC/pjvan_thof/bin/sickle"}
- },
- "star" : {"exe":"test"},
- "bwa" : {"exe":"test"},
- "gatk": {
- "mapping": {
- "flexiprep": {
- }
- },
- "reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
- "dbsnp": "test",
- "hapmap": "test",
- "omni": "test",
- "1000G": "test",
- "mills": "test",
- "haplotypecaller": {
- "stand_call_conf": 20,
- "stand_emit_conf": 20
- }
- },
- "cutadapt": {"exe":"test"},
- "samples": {
- "test": {
- "libraries": {
- "3" : {
- "bam" : "/data/DIV5/SASC/project-072-vcf_Comparison/analysis/runs/01/losekoot_redo_FC59b_L5_I12_S41/run_01/losekoot_redo_FC59b_L5_I12_S41-01.dedup.bam"
- }
- }
- }
- },
- "correct_readgroups": true
-}
diff --git a/public/biopet-framework/examples/gatk-variantcalling.json b/public/biopet-framework/examples/gatk-variantcalling.json
deleted file mode 100644
index 0cab6e62f5971859232cdb867cf33d5f2893fe8d..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/gatk-variantcalling.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
- "reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
- "dbsnp": "bla",
- "haplotypecaller": {
- "stand_call_conf": 20,
- "stand_emit_conf": 20
- },
- "scattercount": 10
-}
diff --git a/public/biopet-framework/examples/gatk-vcf-sample-compare.json b/public/biopet-framework/examples/gatk-vcf-sample-compare.json
deleted file mode 100644
index 89d0d7d92a4cb8fc86a9d0c8d2995227cf7876b0..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/gatk-vcf-sample-compare.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
- "gvcffiles": ["test4.vcf", "test5.vcf"],
- "reference" : "/data/DIV5/SASC/common/gatk_bundle_2.8/hg19/ucsc.hg19.fasta",
- "dbsnp": "bla",
- "haplotypecaller": {
- "stand_call_conf": 20,
- "stand_emit_conf": 20
- }
-}
diff --git a/public/biopet-framework/examples/mapping.json b/public/biopet-framework/examples/mapping.json
deleted file mode 100644
index 5b675451afec13dd438ae1283f1b98dd252e6a4f..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/mapping.json
+++ /dev/null
@@ -1,12 +0,0 @@
-{
- "samtools": {"exe": "test"},
- "reference": "/blabla/blabla.fa",
- "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
- "bwa": { "exe": "test" },
- "flexiprep": {
- "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
- "seqtk": {"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"},
- "cutadapt": {"exe":"/home/pjvan_thof/.local/bin/cutadapt"},
- "sickle": {"exe":"/data/DIV5/SASC/pjvan_thof/bin/sickle"}
- }
-}
diff --git a/public/biopet-framework/examples/sage.json b/public/biopet-framework/examples/sage.json
deleted file mode 100644
index 44d57a292f77d1a0dbdc659b1fab36543cfa3017..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/sage.json
+++ /dev/null
@@ -1,23 +0,0 @@
-{
- "bedtools": {"exe": "test"},
- "samtools": {"exe": "test"},
- "reference": "/blabla/blabla.fa",
- "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
- "bwa": { "exe": "test" },
- "flexiprep": {
- "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
- "seqtk": {"exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"},
- "cutadapt": {"exe":"/home/pjvan_thof/.local/bin/cutadapt"},
- "sickle": {"exe":"/data/DIV5/SASC/pjvan_thof/bin/sickle"}
- },
- "samples": {
- "test": {
- "libraries": {
- "1": {
- "R1": "test.fastq"
- }
- }
- }
- },
- "bowtie": {"exe": "test"}
-}
diff --git a/public/biopet-framework/examples/shark_apps.json b/public/biopet-framework/examples/shark_apps.json
deleted file mode 100644
index d5bd63e020b98f0a01e6e13fc91f556b7578038d..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/shark_apps.json
+++ /dev/null
@@ -1,36 +0,0 @@
-{
- "bwa": {
- "exe": "/usr/local/bwa/bwa-0.7.10/bwa"
- },
- "seqtk": {
- "exe":"/data/DIV5/SASC/common/programs/seqtk/seqtk/seqtk"
- },
- "sickle": {
- "exe":"/data/DIV5/SASC/common/programs/sickle/sickle-1.33/sickle"
- },
- "clever": {
- "exe": "/data/DIV5/SASC/common/programs/clever/clever-toolkit-v2.0rc3/bin/clever",
- "version_exe": "/data/DIV5/SASC/common/programs/clever/clever-toolkit-v2.0rc3/bin/ctk-version"
- },
- "pindel": {
- "exe": "/data/DIV5/SASC/common/programs/pindel/pindel-0.2.5/pindel"
- },
- "breakdancerconfig": {
- "exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/lib/breakdancer-max1.4.4/bam2cfg.pl"
- },
- "breakdancercaller": {
- "exe": "/data/DIV5/SASC/common/programs/breakdancer/breakdancer-v1.4.4/bin/breakdancer-max"
- },
- "fastqc": {
- "exe": "/usr/local/FastQC/FastQC_v0.10.1/fastqc"
- },
- "seqstat": {
- "exe": "/data/DIV5/SASC/common/programs/dQual/fastq-seqstat"
- },
- "stampy": {
- "exe": "/usr/local/stampy/stampy-1.0.23/stampy.py"
- },
- "sambamba": {
- "exe": "/data/DIV5/SASC/common/programs/sambamba/sambamba-0.4.7/build/sambamba"
- }
-}
diff --git a/public/biopet-framework/examples/summaryformat.json b/public/biopet-framework/examples/summaryformat.json
deleted file mode 100644
index be47260b2aec4da6c2b04c46006c6509fa6b8a09..0000000000000000000000000000000000000000
--- a/public/biopet-framework/examples/summaryformat.json
+++ /dev/null
@@ -1,33 +0,0 @@
-{
- "_meta": {},
- "stats": {},
- "resources": {
- "res_key": {
- "uri:": "",
- "md5sum": "",
- "sha256sum": "",
- "adler32sum": ""
- }
- },
- "samples" :{
- "SampleID": {
- "stats": {},
- "resources": {},
- "libraries": {
- "libraryID": {
- "stats": {},
- "resources": {}
- }
- }
- }, "SampleID2": {
- "stats": {},
- "resources": {},
- "libraries": {
- "libraryID": {
- "stats": {},
- "resources": {}
- }
- }
- }
- }
-}
diff --git a/public/biopet-framework/pom.xml b/public/biopet-framework/pom.xml
deleted file mode 100644
index 2517acae3020b2542f7e77f66f9edd522c11c32a..0000000000000000000000000000000000000000
--- a/public/biopet-framework/pom.xml
+++ /dev/null
@@ -1,123 +0,0 @@
-<!--
-
- Biopet is built on top of GATK Queue for building bioinformatic
- pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- should also be able to execute Biopet tools and pipelines.
-
- Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
-
- Contact us at: sasc@lumc.nl
-
- A dual licensing mode is applied. The source code within this project that are
- not part of GATK Queue is freely available for non-commercial use under an AGPL
- license; For commercial users or users who do not want to follow the AGPL
- license, please contact us to obtain a separate license.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
-
- <artifactId>BiopetFramework</artifactId>
- <packaging>jar</packaging>
-
- <parent>
- <groupId>nl.lumc.sasc</groupId>
- <artifactId>Biopet</artifactId>
- <version>0.5.0-SNAPSHOT</version>
- <relativePath>../</relativePath>
- </parent>
-
- <inceptionYear>2014</inceptionYear>
- <name>BiopetFramework</name>
-
- <repositories>
- <repository>
- <id>biojava-maven-repo</id>
- <name>BioJava repository</name>
- <url>http://www.biojava.org/download/maven/</url>
- </repository>
- </repositories>
- <dependencies>
- <dependency>
- <groupId>org.testng</groupId>
- <artifactId>testng</artifactId>
- <version>6.8</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.mockito</groupId>
- <artifactId>mockito-all</artifactId>
- <version>1.9.5</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.10</artifactId>
- <version>2.2.1</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.scala-lang</groupId>
- <artifactId>scala-library</artifactId>
- <version>2.10.4</version>
- </dependency>
- <dependency>
- <groupId>org.broadinstitute.gatk</groupId>
- <artifactId>gatk-queue</artifactId>
- <version>3.4</version>
- </dependency>
- <dependency>
- <groupId>org.broadinstitute.gatk</groupId>
- <artifactId>gatk-queue-extensions-public</artifactId>
- <version>3.4</version>
- </dependency>
- <dependency>
- <groupId>org.broadinstitute.gatk</groupId>
- <artifactId>gatk-utils</artifactId>
- <version>3.4</version>
- <exclusions>
- <exclusion>
- <groupId>org.broadinstitute.gatk</groupId>
- <artifactId>gsalib</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
- <dependency>
- <groupId>io.argonaut</groupId>
- <artifactId>argonaut_2.10</artifactId>
- <version>6.1-M4</version>
- </dependency>
- <dependency>
- <groupId>org.biojava</groupId>
- <artifactId>biojava3-core</artifactId>
- <version>3.1.0</version>
- </dependency>
- <dependency>
- <groupId>org.biojava</groupId>
- <artifactId>biojava3-sequencing</artifactId>
- <version>3.1.0</version>
- </dependency>
- <dependency>
- <groupId>com.google.guava</groupId>
- <artifactId>guava</artifactId>
- <version>18.0</version>
- </dependency>
- <dependency>
- <groupId>com.github.scopt</groupId>
- <artifactId>scopt_2.10</artifactId>
- <version>3.3.0</version>
- </dependency>
- <dependency>
- <groupId>org.scalatra.scalate</groupId>
- <artifactId>scalate-core_2.10</artifactId>
- <version>1.7.0</version>
- </dependency>
- <dependency>
- <groupId>org.yaml</groupId>
- <artifactId>snakeyaml</artifactId>
- <version>1.15</version>
- </dependency>
- </dependencies>
-</project>
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
deleted file mode 100644
index cd45ff92b557b7be4f5fa8ca76030f8b8a2babaf..0000000000000000000000000000000000000000
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+++ /dev/null
@@ -1,92 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.extensions
-
-import java.io.{ File, FileOutputStream }
-
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-
-import scala.sys.process._
-
-/**
- * General rscript extension
- *
- * Created by wyleung on 17-2-15.
- */
-trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
-
- protected var script: File
-
- executable = config("exe", default = "Rscript", submodule = "Rscript")
-
- override def beforeGraph(): Unit = {
- checkScript()
- }
-
- /**
- * If script not exist in file system it try to copy it from the jar
- * @param local if true it use File.createTempFile instead of ".queue/tmp/"
- */
- protected def checkScript(local: Boolean = false): Unit = {
- if (script.exists()) {
- script = script.getAbsoluteFile
- } else {
- val rScript: File = {
- if (local) File.createTempFile(script.getName, ".R")
- else new File(".queue/tmp/" + script)
- }
- if (!rScript.getParentFile.exists) rScript.getParentFile.mkdirs
-
- val is = getClass.getResourceAsStream(script.getPath)
- val os = new FileOutputStream(rScript)
-
- org.apache.commons.io.IOUtils.copy(is, os)
- os.close()
-
- script = rScript
- }
- }
-
- /**
- * Execute rscript on local system
- * @param logger How to handle stdout and stderr
- */
- def runLocal(logger: ProcessLogger): Unit = {
- checkScript(local = true)
-
- this.logger.info(cmdLine)
-
- val cmd = cmdLine.stripPrefix(" '").stripSuffix("' ").split("' *'")
-
- this.logger.info(cmd.mkString(" "))
-
- val process = Process(cmd.toSeq).run(logger)
- this.logger.info(process.exitValue())
- }
-
- /**
- * Execute rscript on local system
- * Stdout and stderr will go to biopet logger
- */
- def runLocal(): Unit = {
- runLocal(ProcessLogger(logger.info(_)))
- }
-
- def cmdLine: String = {
- required(executable) +
- required(script)
- }
-}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
deleted file mode 100644
index 0f0e11c62ac8f935a064b5b3b042d98527e48934..0000000000000000000000000000000000000000
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
+++ /dev/null
@@ -1,80 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.tools
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.ToolCommand
-import nl.lumc.sasc.biopet.utils.ConfigUtils._
-import scala.collection.mutable
-
-import scala.io.Source
-
-/**
- * This tool can convert a tsv to a json file
- */
-object SamplesTsvToJson extends ToolCommand {
- case class Args(inputFiles: List[File] = Nil) extends AbstractArgs
-
- class OptParser extends AbstractOptParser {
- opt[File]('i', "inputFiles") required () unbounded () valueName "<file>" action { (x, c) =>
- c.copy(inputFiles = x :: c.inputFiles)
- } text "Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed"
- }
-
- /** Executes SamplesTsvToJson */
- def main(args: Array[String]): Unit = {
- val argsParser = new OptParser
- val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
-
- val fileMaps = for (inputFile <- commandArgs.inputFiles) yield {
- val reader = Source.fromFile(inputFile)
- val lines = reader.getLines().toList.filter(!_.isEmpty)
- val header = lines.head.split("\t")
- val sampleColumn = header.indexOf("sample")
- val libraryColumn = header.indexOf("library")
- if (sampleColumn == -1) throw new IllegalStateException("Sample column does not exist in: " + inputFile)
-
- val sampleLibCache: mutable.Set[(String, Option[String])] = mutable.Set()
-
- val librariesValues: List[Map[String, Any]] = for (tsvLine <- lines.tail) yield {
- val values = tsvLine.split("\t")
- require(header.length == values.length, "Number of columns is not the same as the header")
- val sample = values(sampleColumn)
- val library = if (libraryColumn != -1) Some(values(libraryColumn)) else None
-
- //FIXME: this is a workaround, should be removed after fixing #180
- if (sample.head.isDigit || library.forall(_.head.isDigit))
- throw new IllegalStateException("Sample or library may not start with a number")
-
- if (sampleLibCache.contains((sample, library)))
- throw new IllegalStateException(s"Combination of $sample and $library is found multiple times")
- else sampleLibCache.add((sample, library))
- val valuesMap = (for (
- t <- 0 until values.size if !values(t).isEmpty && t != sampleColumn && t != libraryColumn
- ) yield header(t) -> values(t)).toMap
- library match {
- case Some(lib) => Map("samples" -> Map(sample -> Map("libraries" -> Map(library -> valuesMap))))
- case _ => Map("samples" -> Map(sample -> valuesMap))
- }
- }
- librariesValues.foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
- }
- val map = fileMaps.foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
- val json = mapToJson(map)
- println(json.spaces2)
- }
-}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
deleted file mode 100644
index 2b47405a46b9971aab59ff2c4eaa088efea7f052..0000000000000000000000000000000000000000
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
+++ /dev/null
@@ -1,84 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.tools
-
-import java.io.File
-import java.nio.file.Paths
-
-import htsjdk.variant.variantcontext.GenotypeType
-import htsjdk.variant.vcf.VCFFileReader
-import org.scalatest.Matchers
-import org.scalatest.mock.MockitoSugar
-import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.Test
-
-import scala.util.Random
-
-/**
- * Test class for [[VcfFilter]]
- *
- * Created by ahbbollen on 9-4-15.
- */
-class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
-
- import VcfFilter._
- private def resourcePath(p: String): String = {
- Paths.get(getClass.getResource(p).toURI).toString
- }
-
- val vepped_path = resourcePath("/VEP_oneline.vcf")
- val vepped = new File(vepped_path)
- val rand = new Random()
-
- @Test def testOutputTypeVcf() = {
- val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf"
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
- main(arguments)
- }
-
- @Test def testOutputTypeBcf() = {
- val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".bcf"
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
- main(arguments)
- }
-
- @Test def testOutputTypeVcfGz() = {
- val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf.gz"
- val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
- main(arguments)
- }
-
- @Test def testHasGenotype() = {
- val reader = new VCFFileReader(vepped, false)
- val record = reader.iterator().next()
-
- hasGenotype(record, List(("Child_7006504", GenotypeType.HET))) shouldBe true
- hasGenotype(record, List(("Child_7006504", GenotypeType.HOM_VAR))) shouldBe false
- hasGenotype(record, List(("Child_7006504", GenotypeType.HOM_REF))) shouldBe false
- hasGenotype(record, List(("Child_7006504", GenotypeType.NO_CALL))) shouldBe false
- hasGenotype(record, List(("Child_7006504", GenotypeType.MIXED))) shouldBe false
-
- hasGenotype(record, List(("Mother_7006508", GenotypeType.HET))) shouldBe false
- hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_VAR))) shouldBe false
- hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_REF))) shouldBe true
- hasGenotype(record, List(("Mother_7006508", GenotypeType.NO_CALL))) shouldBe false
- hasGenotype(record, List(("Mother_7006508", GenotypeType.MIXED))) shouldBe false
-
- hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_REF), ("Child_7006504", GenotypeType.HET))) shouldBe true
- hasGenotype(record, List(("Mother_7006508", GenotypeType.HET), ("Child_7006504", GenotypeType.HOM_REF))) shouldBe false
- }
-
-}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
deleted file mode 100644
index 0ffe4713b117f8797be7b075e5a948bb0f709722..0000000000000000000000000000000000000000
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
+++ /dev/null
@@ -1,119 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.tools
-
-import htsjdk.variant.variantcontext.Allele
-import nl.lumc.sasc.biopet.tools.VcfStats._
-import org.scalatest.Matchers
-import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.Test
-
-import scala.collection.mutable
-
-/**
- * Test class for [[VcfStats]]
- *
- * Created by pjvan_thof on 2/5/15.
- */
-class VcfStatsTest extends TestNGSuite with Matchers {
-
- @Test
- def testSampleToSampleStats(): Unit = {
- val s1 = SampleToSampleStats()
- val s2 = SampleToSampleStats()
- s1.alleleOverlap shouldBe 0
- s1.genotypeOverlap shouldBe 0
- s2.alleleOverlap shouldBe 0
- s2.genotypeOverlap shouldBe 0
-
- s1 += s2
- s1.alleleOverlap shouldBe 0
- s1.genotypeOverlap shouldBe 0
- s2.alleleOverlap shouldBe 0
- s2.genotypeOverlap shouldBe 0
-
- s2.alleleOverlap = 2
- s2.genotypeOverlap = 3
-
- s1 += s2
- s1.alleleOverlap shouldBe 2
- s1.genotypeOverlap shouldBe 3
- s2.alleleOverlap shouldBe 2
- s2.genotypeOverlap shouldBe 3
-
- s1 += s2
- s1.alleleOverlap shouldBe 4
- s1.genotypeOverlap shouldBe 6
- s2.alleleOverlap shouldBe 2
- s2.genotypeOverlap shouldBe 3
- }
-
- @Test
- def testSampleStats(): Unit = {
- val s1 = SampleStats()
- val s2 = SampleStats()
-
- s1.sampleToSample += "s1" -> SampleToSampleStats()
- s1.sampleToSample += "s2" -> SampleToSampleStats()
- s2.sampleToSample += "s1" -> SampleToSampleStats()
- s2.sampleToSample += "s2" -> SampleToSampleStats()
-
- s1.sampleToSample("s1").alleleOverlap = 1
- s2.sampleToSample("s2").alleleOverlap = 2
-
- val bla1 = s1.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) += "1" -> mutable.Map(1 -> 1)
- s1.genotypeStats += "chr" -> bla1
- val bla2 = s2.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) += "2" -> mutable.Map(2 -> 2)
- s2.genotypeStats += "chr" -> bla2
-
- val ss1 = SampleToSampleStats()
- val ss2 = SampleToSampleStats()
-
- s1 += s2
- s1.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) shouldBe mutable.Map("1" -> mutable.Map(1 -> 1), "2" -> mutable.Map(2 -> 2))
- ss1.alleleOverlap = 1
- ss2.alleleOverlap = 2
- s1.sampleToSample shouldBe mutable.Map("s1" -> ss1, "s2" -> ss2)
-
- s1 += s2
- s1.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) shouldBe mutable.Map("1" -> mutable.Map(1 -> 1), "2" -> mutable.Map(2 -> 4))
-
- s1 += s1
- s1.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) shouldBe mutable.Map("1" -> mutable.Map(1 -> 2), "2" -> mutable.Map(2 -> 8))
- }
-
- @Test
- def testAlleleOverlap(): Unit = {
-
- val a1 = Allele.create("G")
- val a2 = Allele.create("A")
-
- alleleOverlap(List(a1, a1), List(a1, a1)) shouldBe 2
- alleleOverlap(List(a2, a2), List(a2, a2)) shouldBe 2
- alleleOverlap(List(a1, a2), List(a1, a2)) shouldBe 2
- alleleOverlap(List(a1, a2), List(a2, a1)) shouldBe 2
- alleleOverlap(List(a2, a1), List(a1, a2)) shouldBe 2
- alleleOverlap(List(a2, a1), List(a2, a1)) shouldBe 2
-
- alleleOverlap(List(a1, a2), List(a1, a1)) shouldBe 1
- alleleOverlap(List(a2, a1), List(a1, a1)) shouldBe 1
- alleleOverlap(List(a1, a1), List(a1, a2)) shouldBe 1
- alleleOverlap(List(a1, a1), List(a2, a1)) shouldBe 1
-
- alleleOverlap(List(a1, a1), List(a2, a2)) shouldBe 0
- alleleOverlap(List(a2, a2), List(a1, a1)) shouldBe 0
- }
-}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
deleted file mode 100644
index 9996dfed3befed4e8913ee1377d04953607dfbc9..0000000000000000000000000000000000000000
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+++ /dev/null
@@ -1,62 +0,0 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.tools
-
-import java.io.File
-import java.nio.file.Paths
-
-import org.scalatest.Matchers
-import org.scalatest.mock.MockitoSugar
-import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.Test
-
-import scala.util.Random
-
-/**
- * Test class for [[VcfWithVcfTest]]
- *
- * Created by ahbbollen on 10-4-15.
- */
-class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
- import VcfWithVcf._
-
- private def resourcePath(p: String): String = {
- Paths.get(getClass.getResource(p).toURI).toString
- }
-
- val veppedPath = resourcePath("/VEP_oneline.vcf.gz")
- val unveppedPath = resourcePath("/unvepped.vcf.gz")
- val rand = new Random()
-
- @Test def testOutputTypeVcf() = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
- val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
- main(arguments)
- }
-
- @Test def testOutputTypeVcfGz() = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
- val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
- main(arguments)
- }
-
- @Test def testOutputTypeBcf() = {
- val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
- val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
- main(arguments)
- }
-
-}
diff --git a/public/biopet-public-package/pom.xml b/public/biopet-public-package/pom.xml
index aacfc8125bff7a412aa704ee450b3aa0146df0b7..aeed0caa9f6639b0a08f71a3fd0ac6ca646c506c 100644
--- a/public/biopet-public-package/pom.xml
+++ b/public/biopet-public-package/pom.xml
@@ -35,13 +35,13 @@
<properties>
<sting.shade.phase>package</sting.shade.phase>
- <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutablePublic</app.main.class>
+ <app.main.class>nl.lumc.sasc.biopet.BiopetExecutablePublic</app.main.class>
</properties>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
similarity index 96%
rename from public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
rename to public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
index 40012aa2759279307589ef9309474f9841d34921..36770bb18747691afc468bf7cdff14d444478b81 100644
--- a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
+++ b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
@@ -13,7 +13,9 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet
+
+import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
object BiopetExecutablePublic extends BiopetExecutable {
def publicPipelines: List[MainCommand] = List(
diff --git a/public/biopet-tools-extensions/pom.xml b/public/biopet-tools-extensions/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e8ef9d9a7b4f21a2dada57c3cb1cfcfe0299dd12
--- /dev/null
+++ b/public/biopet-tools-extensions/pom.xml
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <parent>
+ <artifactId>Biopet</artifactId>
+ <groupId>nl.lumc.sasc</groupId>
+ <version>0.5.0-SNAPSHOT</version>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+
+ <artifactId>BiopetToolsExtensions</artifactId>
+
+ <dependencies>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetCore</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetExtensions</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetTools</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
\ No newline at end of file
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
new file mode 100644
index 0000000000000000000000000000000000000000..9b0020ae21e8626f3f987aaec2d1bd2921374bed
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
@@ -0,0 +1,70 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
+ def toolObject = nl.lumc.sasc.biopet.tools.BastyGenerateFasta
+
+ @Input(doc = "Input vcf file", required = false)
+ var inputVcf: File = _
+
+ @Input(doc = "Bam File", required = false)
+ var bamFile: File = _
+
+ @Input(doc = "reference", required = false)
+ var reference: File = _
+
+ @Output(doc = "Output fasta, variants only", required = false)
+ var outputVariants: File = _
+
+ @Output(doc = "Output fasta, variants only", required = false)
+ var outputConsensus: File = _
+
+ @Output(doc = "Output fasta, variants only", required = false)
+ var outputConsensusVariants: File = _
+
+ var snpsOnly: Boolean = config("snps_only", default = false)
+ var sampleName: String = _
+ var minAD: Int = config("min_ad", default = 8)
+ var minDepth: Int = config("min_depth", default = 8)
+ var outputName: String = _
+
+ override def defaultCoreMemory = 4.0
+
+ override def beforeGraph(): Unit = {
+ super.beforeGraph()
+ reference = referenceFasta()
+ }
+
+ override def commandLine = super.commandLine +
+ optional("--inputVcf", inputVcf) +
+ optional("--bamFile", bamFile) +
+ optional("--outputVariants", outputVariants) +
+ optional("--outputConsensus", outputConsensus) +
+ optional("--outputConsensusVariants", outputConsensusVariants) +
+ conditional(snpsOnly, "--snpsOnly") +
+ optional("--sampleName", sampleName) +
+ required("--outputName", outputName) +
+ optional("--minAD", minAD) +
+ optional("--minDepth", minDepth) +
+ optional("--reference", reference)
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
new file mode 100644
index 0000000000000000000000000000000000000000..bab2f7c0ae0fa260a78ff366d9e9f4a6c177d9f6
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
@@ -0,0 +1,52 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * @deprecated Use picard.util.BedToIntervalList instead
+ */
+class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.BedToInterval
+
+ @Input(doc = "Input Bed file", required = true)
+ var input: File = _
+
+ @Input(doc = "Bam File", required = true)
+ var bamFile: File = _
+
+ @Output(doc = "Output interval list", required = true)
+ var output: File = _
+
+ override def defaultCoreMemory = 1.0
+
+ override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
+}
+
+object BedToInterval {
+ def apply(root: Configurable, inputBed: File, inputBam: File, output: File): BedToInterval = {
+ val bedToInterval = new BedToInterval(root)
+ bedToInterval.input = inputBed
+ bedToInterval.bamFile = inputBam
+ bedToInterval.output = output
+ bedToInterval
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
new file mode 100644
index 0000000000000000000000000000000000000000..817b6d3f2792168a8f4fdf8549fa3c16c858e21e
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
@@ -0,0 +1,38 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts
+
+ @Input(doc = "Input fasta", shortName = "input", required = true)
+ var input: File = _
+
+ @Output(doc = "Output tag library", shortName = "output", required = true)
+ var output: File = _
+
+ override def defaultCoreMemory = 3.0
+
+ override def commandLine = super.commandLine +
+ required("-I", input) +
+ required("-o", output)
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
new file mode 100644
index 0000000000000000000000000000000000000000..ff06bc963764f07563aa4ca0e2926119ba667c9b
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
@@ -0,0 +1,57 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
+ def toolObject = nl.lumc.sasc.biopet.tools.BiopetFlagstat
+
+ @Input(doc = "Input bam", shortName = "input", required = true)
+ var input: File = _
+
+ @Output(doc = "Output flagstat", shortName = "output", required = true)
+ var output: File = _
+
+ @Output(doc = "summary output file", shortName = "output", required = false)
+ var summaryFile: File = _
+
+ override def defaultCoreMemory = 6.0
+
+ override def commandLine = super.commandLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
+
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = {
+ ConfigUtils.fileToConfigMap(summaryFile)
+ }
+}
+
+object BiopetFlagstat {
+ def apply(root: Configurable, input: File, outputDir: File): BiopetFlagstat = {
+ val flagstat = new BiopetFlagstat(root)
+ flagstat.input = input
+ flagstat.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat")
+ flagstat.summaryFile = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat.json")
+ flagstat
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
new file mode 100644
index 0000000000000000000000000000000000000000..df7e32e19bacfc8021ec015fcf019f9f16f61fe2
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
@@ -0,0 +1,43 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Queue extension for the FastqSplitter
+ * @param root Parent object
+ */
+class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.FastqSplitter
+
+ @Input(doc = "Input fastq", shortName = "input", required = true)
+ var input: File = _
+
+ @Output(doc = "Output fastq files", shortName = "output", required = true)
+ var output: List[File] = Nil
+
+ override def defaultCoreMemory = 4.0
+
+ /** * Generate command to execute */
+ override def commandLine = super.commandLine +
+ required("-I", input) +
+ repeat("-o", output)
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
new file mode 100644
index 0000000000000000000000000000000000000000..90100c8e7942afe8dd105ca64ba2ff5990747b7f
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
@@ -0,0 +1,99 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import scala.io.Source
+import scala.util.matching.Regex
+
+/**
+ * FastqSync function class for usage in Biopet pipelines
+ *
+ * @param root Configuration object for the pipeline
+ */
+class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summarizable {
+
+ def toolObject = nl.lumc.sasc.biopet.tools.FastqSync
+
+ @Input(doc = "Original FASTQ file (read 1 or 2)", shortName = "r", required = true)
+ var refFastq: File = null
+
+ @Input(doc = "Input read 1 FASTQ file", shortName = "i", required = true)
+ var inputFastq1: File = null
+
+ @Input(doc = "Input read 2 FASTQ file", shortName = "j", required = true)
+ var inputFastq2: File = null
+
+ @Output(doc = "Output read 1 FASTQ file", shortName = "o", required = true)
+ var outputFastq1: File = null
+
+ @Output(doc = "Output read 2 FASTQ file", shortName = "p", required = true)
+ var outputFastq2: File = null
+
+ @Output(doc = "Sync statistics", required = true)
+ var outputStats: File = null
+
+ override def defaultCoreMemory = 4.0
+
+ // executed command line
+ override def commandLine =
+ super.commandLine +
+ required("-r", refFastq) +
+ required("-i", inputFastq1) +
+ required("-j", inputFastq2) +
+ required("-o", outputFastq1) +
+ required("-p", outputFastq2) + " > " +
+ required(outputStats)
+
+ def summaryFiles: Map[String, File] = Map()
+
+ def summaryStats: Map[String, Any] = {
+ val regex = new Regex("""Filtered (\d*) reads from first read file.
+ |Filtered (\d*) reads from second read file.
+ |Synced read files contain (\d*) reads.""".stripMargin,
+ "R1", "R2", "RL")
+
+ val (countFilteredR1, countFilteredR2, countRLeft) =
+ if (outputStats.exists) {
+ val text = Source
+ .fromFile(outputStats)
+ .getLines()
+ .mkString("\n")
+ regex.findFirstMatchIn(text) match {
+ case None => (0, 0, 0)
+ case Some(rmatch) => (rmatch.group("R1").toInt, rmatch.group("R2").toInt, rmatch.group("RL").toInt)
+ }
+ } else (0, 0, 0)
+
+ Map("num_reads_discarded_R1" -> countFilteredR1,
+ "num_reads_discarded_R2" -> countFilteredR2,
+ "num_reads_kept" -> countRLeft
+ )
+ }
+
+ override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
+ (v1, v2) match {
+ case (v1: Int, v2: Int) => v1 + v2
+ case _ => v1
+ }
+ }
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
new file mode 100644
index 0000000000000000000000000000000000000000..eedb51fdd1bb9d07d405299cb9dbf913681fbb96
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
@@ -0,0 +1,59 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.MergeAlleles
+
+ @Input(doc = "Input vcf files", shortName = "input", required = true)
+ var input: List[File] = Nil
+
+ @Output(doc = "Output vcf file", shortName = "output", required = true)
+ var output: File = _
+
+ @Output(doc = "Output vcf file index", shortName = "output", required = true)
+ private var outputIndex: File = _
+
+ var reference: File = config("reference")
+
+ override def defaultCoreMemory = 1.0
+
+ override def beforeGraph() {
+ super.beforeGraph()
+ if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
+ if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
+ }
+
+ override def commandLine = super.commandLine +
+ repeat("-I", input) +
+ required("-o", output) +
+ required("-R", reference)
+}
+
+object MergeAlleles {
+ def apply(root: Configurable, input: List[File], output: File): MergeAlleles = {
+ val mergeAlleles = new MergeAlleles(root)
+ mergeAlleles.input = input
+ mergeAlleles.output = output
+ mergeAlleles
+ }
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
new file mode 100644
index 0000000000000000000000000000000000000000..96a421db3e706d0220df76b6acfd5aab9cda9480
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
@@ -0,0 +1,79 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import scala.collection.mutable.{ Set => MutSet }
+
+/**
+ * Biopet wrapper for the [[MergeTables]] command line tool.
+ *
+ * @param root [[Configurable]] object
+ */
+class MergeTables(val root: Configurable) extends ToolCommandFuntion {
+
+ def toolObject = nl.lumc.sasc.biopet.tools.MergeTables
+
+ override def defaultCoreMemory = 6.0
+
+ /** List of input tabular files */
+ @Input(doc = "Input table files", required = true)
+ var inputTables: List[File] = List.empty[File]
+
+ /** Output file */
+ @Output(doc = "Output merged table", required = true)
+ var output: File = null
+
+ // TODO: should be List[Int] really
+ /** List of column indices to combine to make a unique identifier per row */
+ var idColumnIndices: List[String] = config("id_column_indices", default = List("1"))
+
+ /** Index of column from each tabular file containing the values to be put in the final merged table */
+ var valueColumnIndex: Int = config("value_column_index", default = 2)
+
+ /** Name of the identifier column in the output file */
+ var idColumnName: Option[String] = config("id_column_name")
+
+ /** Common file extension of all input files */
+ var fileExtension: Option[String] = config("file_extension")
+
+ /** Number of header lines from each input file to ignore */
+ var numHeaderLines: Option[Int] = config("num_header_lines")
+
+ /** String to use when a value is missing from an input file */
+ var fallbackString: Option[String] = config("fallback_string")
+
+ /** Column delimiter of each input file (used for splitting into columns */
+ var delimiter: Option[String] = config("delimiter")
+
+ // executed command line
+ override def commandLine =
+ super.commandLine +
+ required("-i", idColumnIndices.mkString(",")) +
+ required("-a", valueColumnIndex) +
+ optional("-n", idColumnName) +
+ optional("-e", fileExtension) +
+ optional("-m", numHeaderLines) +
+ optional("-f", fallbackString) +
+ optional("-d", delimiter) +
+ required("-o", output) +
+ required("", repeat(inputTables), escape = false)
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
new file mode 100644
index 0000000000000000000000000000000000000000..5a3e1e3f26588c103a4bf5e0a190aa223d064450
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
@@ -0,0 +1,85 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import scala.collection.JavaConversions._
+
+class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
+ def toolObject = nl.lumc.sasc.biopet.tools.MpileupToVcf
+
+ @Input(doc = "Input mpileup file", shortName = "mpileup", required = false)
+ var inputMpileup: File = _
+
+ @Input(doc = "Input bam file", shortName = "bam", required = false)
+ var inputBam: File = _
+
+ @Output(doc = "Output tag library", shortName = "output", required = true)
+ var output: File = _
+
+ var minDP: Option[Int] = config("min_dp")
+ var minAP: Option[Int] = config("min_ap")
+ var homoFraction: Option[Double] = config("homoFraction")
+ var ploidy: Option[Int] = config("ploidy")
+ var sample: String = _
+ var reference: String = _
+
+ override def defaultCoreMemory = 3.0
+
+ override def defaults = ConfigUtils.mergeMaps(Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1)),
+ super.defaults)
+
+ override def beforeGraph() {
+ super.beforeGraph()
+ reference = referenceFasta().getAbsolutePath
+ val samtoolsMpileup = new SamtoolsMpileup(this)
+ }
+
+ override def beforeCmd(): Unit = {
+ if (sample == null && inputBam.exists()) {
+ val inputSam = SamReaderFactory.makeDefault.open(inputBam)
+ val readGroups = inputSam.getFileHeader.getReadGroups
+ val samples = readGroups.map(readGroup => readGroup.getSample).distinct
+ sample = samples.head
+ inputSam.close()
+ }
+ }
+
+ override def commandLine = {
+ (if (inputMpileup == null) {
+ val samtoolsMpileup = new SamtoolsMpileup(this)
+ samtoolsMpileup.reference = referenceFasta()
+ samtoolsMpileup.input = List(inputBam)
+ samtoolsMpileup.cmdPipe + " | "
+ } else "") +
+ super.commandLine +
+ required("-o", output) +
+ optional("--minDP", minDP) +
+ optional("--minAP", minAP) +
+ optional("--homoFraction", homoFraction) +
+ optional("--ploidy", ploidy) +
+ required("--sample", sample) +
+ (if (inputBam == null) required("-I", inputMpileup) else "")
+ }
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
new file mode 100644
index 0000000000000000000000000000000000000000..302aa11586119a6602f29b0b452ed0645aeb2c37
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
@@ -0,0 +1,68 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+
+/**
+ * Queue class for PrefixFastq tool
+ *
+ * Created by pjvan_thof on 1/13/15.
+ */
+class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.PrefixFastq
+
+ override def defaultCoreMemory = 1.0
+
+ @Input(doc = "Input fastq", shortName = "I", required = true)
+ var inputFastq: File = _
+
+ @Output(doc = "Output fastq", shortName = "o", required = true)
+ var outputFastq: File = _
+
+ @Argument(doc = "Prefix seq", required = true)
+ var prefixSeq: String = _
+
+ /**
+ * Creates command to execute extension
+ * @return
+ */
+ override def commandLine = super.commandLine +
+ required("-i", inputFastq) +
+ required("-o", outputFastq) +
+ optional("-s", prefixSeq)
+}
+
+object PrefixFastq {
+ /**
+ * Create a PrefixFastq class object with a sufix ".prefix.fastq" in the output folder
+ *
+ * @param root parent object
+ * @param input input file
+ * @param outputDir outputFolder
+ * @return PrefixFastq class object
+ */
+ def apply(root: Configurable, input: File, outputDir: String): PrefixFastq = {
+ val prefixFastq = new PrefixFastq(root)
+ prefixFastq.inputFastq = input
+ prefixFastq.outputFastq = new File(outputDir, input.getName + ".prefix.fastq")
+ prefixFastq
+ }
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
new file mode 100644
index 0000000000000000000000000000000000000000..2ee9d97e17ef35cbf6573bf0fa91bb5fc8f76b2c
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
@@ -0,0 +1,38 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.SageCountFastq
+
+ @Input(doc = "Input fasta", shortName = "input", required = true)
+ var input: File = _
+
+ @Output(doc = "Output tag library", shortName = "output", required = true)
+ var output: File = _
+
+ override def defaultCoreMemory = 3.0
+
+ override def commandLine = super.commandLine +
+ required("-I", input) +
+ required("-o", output)
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
new file mode 100644
index 0000000000000000000000000000000000000000..4b287d2cefaf98c777ca2ad44084f74bfacf5047
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
@@ -0,0 +1,54 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.SageCreateLibrary
+
+ @Input(doc = "Input fasta", shortName = "input", required = true)
+ var input: File = _
+
+ @Output(doc = "Output tag library", shortName = "output", required = true)
+ var output: File = _
+
+ @Output(doc = "Output no tags", shortName = "noTagsOutput", required = false)
+ var noTagsOutput: File = _
+
+ @Output(doc = "Output no anti tags library", shortName = "noAntiTagsOutput", required = false)
+ var noAntiTagsOutput: File = _
+
+ @Output(doc = "Output file all genes", shortName = "allGenes", required = false)
+ var allGenesOutput: File = _
+
+ var tag: String = config("tag", default = "CATG")
+ var length: Option[Int] = config("length", default = 17)
+
+ override def defaultCoreMemory = 3.0
+
+ override def commandLine = super.commandLine +
+ required("-I", input) +
+ optional("--tag", tag) +
+ optional("--length", length) +
+ optional("--noTagsOutput", noTagsOutput) +
+ optional("--noAntiTagsOutput", noAntiTagsOutput) +
+ required("-o", output)
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
new file mode 100644
index 0000000000000000000000000000000000000000..d0779973b4484f29264bc574af6d898e1df8804d
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
@@ -0,0 +1,54 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.SageCreateTagCounts
+
+ @Input(doc = "Raw count file", shortName = "input", required = true)
+ var input: File = _
+
+ @Input(doc = "tag library", shortName = "taglib", required = true)
+ var tagLib: File = _
+
+ @Output(doc = "Sense count file", shortName = "sense", required = true)
+ var countSense: File = _
+
+ @Output(doc = "Sense all count file", shortName = "allsense", required = true)
+ var countAllSense: File = _
+
+ @Output(doc = "AntiSense count file", shortName = "antisense", required = true)
+ var countAntiSense: File = _
+
+ @Output(doc = "AntiSense all count file", shortName = "allantisense", required = true)
+ var countAllAntiSense: File = _
+
+ override def defaultCoreMemory = 3.0
+
+ override def commandLine = super.commandLine +
+ required("-I", input) +
+ required("--tagLib", tagLib) +
+ optional("--countSense", countSense) +
+ optional("--countAllSense", countAllSense) +
+ optional("--countAntiSense", countAntiSense) +
+ optional("--countAllAntiSense", countAllAntiSense)
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
new file mode 100644
index 0000000000000000000000000000000000000000..cc7a8e6ede5bb1ba0d318639e8b9320a0ae8024a
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
@@ -0,0 +1,64 @@
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Seqstat function class for usage in Biopet pipelines
+ *
+ * @param root Configuration object for the pipeline
+ */
+class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
+ def toolObject = nl.lumc.sasc.biopet.tools.SeqStat
+
+ @Input(doc = "Input FASTQ", shortName = "input", required = true)
+ var input: File = null
+
+ @Output(doc = "Output JSON", shortName = "output", required = true)
+ var output: File = null
+
+ override def defaultCoreMemory = 2.5
+
+ override def commandLine = super.commandLine + required("-i", input) + required("-o", output)
+
+ def summaryStats: Map[String, Any] = {
+ val map = ConfigUtils.fileToConfigMap(output)
+
+ ConfigUtils.any2map(map.getOrElse("stats", Map()))
+ }
+
+ def summaryFiles: Map[String, File] = Map()
+
+ override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
+ (v1, v2) match {
+ case (v1: Array[_], v2: Array[_]) => v1.zip(v2).map(v => resolveSummaryConflict(v._1, v._2, key))
+ case (v1: List[_], v2: List[_]) => v1.zip(v2).map(v => resolveSummaryConflict(v._1, v._2, key))
+ case (v1: Int, v2: Int) if key == "len_min" => if (v1 < v2) v1 else v2
+ case (v1: Int, v2: Int) if key == "len_max" => if (v1 > v2) v1 else v2
+ case (v1: Int, v2: Int) => v1 + v2
+ case (v1: Long, v2: Long) => v1 + v2
+ case _ => v1
+ }
+ }
+}
+
+object SeqStat {
+ def apply(root: Configurable, input: File, output: File): SeqStat = {
+ val seqstat = new SeqStat(root)
+ seqstat.input = input
+ seqstat.output = new File(output, input.getName.substring(0, input.getName.lastIndexOf(".")) + ".seqstats.json")
+ seqstat
+ }
+
+ def apply(root: Configurable, fastqfile: File, outDir: String): SeqStat = {
+ val seqstat = new SeqStat(root)
+ seqstat.input = fastqfile
+ seqstat.output = new File(outDir, fastqfile.getName.substring(0, fastqfile.getName.lastIndexOf(".")) + ".seqstats.json")
+ seqstat
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
new file mode 100644
index 0000000000000000000000000000000000000000..558c93f8532b95ccd3dfa33e3265f0fbebda8104
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
@@ -0,0 +1,27 @@
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Created by pjvanthof on 22/08/15.
+ */
+class SquishBed(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.SquishBed
+
+ @Input(doc = "Input Bed file", required = true)
+ var input: File = _
+
+ @Output(doc = "Output interval list", required = true)
+ var output: File = _
+
+ var strandSensitive: Boolean = config("strandSensitive", default = false)
+
+ override def commandLine = super.commandLine +
+ required("-I", input) +
+ required("-o", output) +
+ conditional(strandSensitive, "-s")
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
new file mode 100644
index 0000000000000000000000000000000000000000..60d550532dfd30150e63f11096237356aa182a1a
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
@@ -0,0 +1,49 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.VcfFilter
+
+ @Input(doc = "Input vcf", shortName = "I", required = true)
+ var inputVcf: File = _
+
+ @Output(doc = "Output vcf", shortName = "o", required = false)
+ var outputVcf: File = _
+
+ var minSampleDepth: Option[Int] = config("min_sample_depth")
+ var minTotalDepth: Option[Int] = config("min_total_depth")
+ var minAlternateDepth: Option[Int] = config("min_alternate_depth")
+ var minSamplesPass: Option[Int] = config("min_samples_pass")
+ var filterRefCalls: Boolean = config("filter_ref_calls", default = false)
+
+ override def defaultCoreMemory = 3.0
+
+ override def commandLine = super.commandLine +
+ required("-I", inputVcf) +
+ required("-o", outputVcf) +
+ optional("--minSampleDepth", minSampleDepth) +
+ optional("--minTotalDepth", minTotalDepth) +
+ optional("--minAlternateDepth", minAlternateDepth) +
+ optional("--minSamplesPass", minSamplesPass) +
+ conditional(filterRefCalls, "--filterRefCalls")
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
new file mode 100644
index 0000000000000000000000000000000000000000..3fd09a67fb74b3759ec3f00c51344f88afc53231
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
@@ -0,0 +1,113 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import scala.io.Source
+
+/**
+ * This tool will generate statistics from a vcf file
+ *
+ * Created by pjvan_thof on 1/10/15.
+ */
+class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable with Reference {
+ def toolObject = nl.lumc.sasc.biopet.tools.VcfStats
+
+ @Input(doc = "Input fastq", shortName = "I", required = true)
+ var input: File = _
+
+ @Input
+ protected var index: File = null
+
+ @Output
+ protected var generalStats: File = null
+
+ @Output
+ protected var genotypeStats: File = null
+
+ override def defaultCoreMemory = 3.0
+ override def defaultThreads = 3
+
+ protected var outputDir: File = _
+
+ var infoTags: List[String] = Nil
+ var genotypeTags: List[String] = Nil
+ var allInfoTags = false
+ var allGenotypeTags = false
+ var reference: File = _
+
+ override def beforeGraph(): Unit = {
+ reference = referenceFasta()
+ index = new File(input.getAbsolutePath + ".tbi")
+ }
+
+ /** Set output dir and a output file */
+ def setOutputDir(dir: File): Unit = {
+ outputDir = dir
+ generalStats = new File(dir, "general.tsv")
+ genotypeStats = new File(dir, "genotype-general.tsv")
+ jobOutputFile = new File(dir, ".vcfstats.out")
+ }
+
+ /** Creates command to execute extension */
+ override def commandLine = super.commandLine +
+ required("-I", input) +
+ required("-o", outputDir) +
+ repeat("--infoTag", infoTags) +
+ repeat("--genotypeTag", genotypeTags) +
+ conditional(allInfoTags, "--allInfoTags") +
+ conditional(allGenotypeTags, "--allGenotypeTags") +
+ required("-R", reference)
+
+ /** Returns general stats to the summary */
+ def summaryStats: Map[String, Any] = {
+ Map("info" -> (for (
+ line <- Source.fromFile(generalStats).getLines().toList.tail;
+ values = line.split("\t") if values.size >= 2 && !values(0).isEmpty
+ ) yield values(0) -> values(1).toInt
+ ).toMap)
+ }
+
+ /** return only general files to summary */
+ def summaryFiles: Map[String, File] = Map(
+ "general_stats" -> generalStats,
+ "genotype_stats" -> genotypeStats
+ )
+
+ override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
+ val data = Source.fromFile(genotypeStats).getLines().map(_.split("\t")).toArray
+
+ for (s <- 1 until data(0).size) {
+ val sample = data(0)(s)
+ val stats = Map("genotype" -> (for (f <- 1 until data.length) yield {
+ data(f)(0) -> data(f)(s)
+ }).toMap)
+
+ val sum = new Summarizable {
+ override def summaryFiles: Map[String, File] = Map()
+ override def summaryStats: Map[String, Any] = stats
+ }
+
+ qscript.addSummarizable(sum, name, Some(sample))
+ }
+ }
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
new file mode 100644
index 0000000000000000000000000000000000000000..5ab877502eaef6133b51a1927c83b94dc5b7b3ba
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
@@ -0,0 +1,58 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Biopet extension for tool VcfWithVcf
+ */
+class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.VcfWithVcf
+
+ @Input(doc = "Input vcf file", shortName = "input", required = true)
+ var input: File = _
+
+ @Input(doc = "Secondary vcf file", shortName = "secondary", required = true)
+ var secondaryVcf: File = _
+
+ @Output(doc = "Output vcf file", shortName = "output", required = true)
+ var output: File = _
+
+ @Output(doc = "Output vcf file index", shortName = "output", required = true)
+ private var outputIndex: File = _
+
+ var fields: List[(String, String, Option[String])] = List()
+
+ override def defaultCoreMemory = 2.0
+
+ override def beforeGraph() {
+ super.beforeGraph()
+ if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
+ if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
+ if (fields.isEmpty) throw new IllegalArgumentException("No fields found for VcfWithVcf")
+ }
+
+ override def commandLine = super.commandLine +
+ required("-I", input) +
+ required("-o", output) +
+ required("-s", secondaryVcf) +
+ repeat("-f", fields.map(x => x._1 + ":" + x._2 + ":" + x._3.getOrElse("none")))
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
new file mode 100644
index 0000000000000000000000000000000000000000..4379b990dd585b012b15a44a7fc0605a7772b898
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
@@ -0,0 +1,53 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * This tool parses a VEP annotated VCF into a standard VCF file.
+ * The VEP puts all its annotations for each variant in an CSQ string, where annotations per transcript are comma-separated
+ * Annotations are then furthermore pipe-separated.
+ * This tool has two modes:
+ * 1) explode - explodes all transcripts such that each is on a unique line
+ * 2) standard - parse as a standard VCF, where multiple transcripts occur in the same line
+ * Created by ahbbollen on 10/27/14.
+ */
+
+class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.VepNormalizer
+
+ @Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
+ var inputVCF: File = null
+
+ @Output(doc = "Output VCF", shortName = "OutputFile", required = true)
+ var outputVcf: File = null
+
+ var mode: String = config("mode", default = "standard")
+ var doNotRemove: Boolean = config("do_not_remove", default = false)
+
+ override def defaultCoreMemory = 4.0
+
+ override def commandLine = super.commandLine +
+ required("-I", inputVCF) +
+ required("-O", outputVcf) +
+ required("-m", mode) +
+ conditional(doNotRemove, "--do-not-remove")
+}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
new file mode 100644
index 0000000000000000000000000000000000000000..1e468bd36ac52bed889ccc0871a092316def63f0
--- /dev/null
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
@@ -0,0 +1,45 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+// TODO: finish implementation for usage in pipelines
+/**
+ * WipeReads function class for usage in Biopet pipelines
+ *
+ * @param root Configuration object for the pipeline
+ */
+class WipeReads(val root: Configurable) extends ToolCommandFuntion {
+
+ def toolObject = nl.lumc.sasc.biopet.tools.WipeReads
+
+ @Input(doc = "Input BAM file (must be indexed)", shortName = "I", required = true)
+ var inputBam: File = null
+
+ @Input(doc = "Interval file", shortName = "r", required = true)
+ var intervalFile: File = null
+
+ @Output(doc = "Output BAM", shortName = "o", required = true)
+ var outputBam: File = null
+
+ @Output(doc = "BAM containing discarded reads", shortName = "f", required = false)
+ var discardedBam: File = null
+}
diff --git a/public/biopet-tools-package/pom.xml b/public/biopet-tools-package/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8801d9280163613168001738d1a6c44c2fc22d2c
--- /dev/null
+++ b/public/biopet-tools-package/pom.xml
@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <parent>
+ <artifactId>Biopet</artifactId>
+ <groupId>nl.lumc.sasc</groupId>
+ <version>0.5.0-SNAPSHOT</version>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+
+ <artifactId>BiopetToolsPackage</artifactId>
+
+ <properties>
+ <sting.shade.phase>package</sting.shade.phase>
+ <app.main.class>nl.lumc.sasc.biopet.BiopetToolsExecutable</app.main.class>
+ </properties>
+
+ <dependencies>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetTools</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <version>2.4.1</version>
+ <configuration>
+ <!--suppress MavenModelInspection -->
+ <finalName>BiopetTools-${project.version}-${git.commit.id.abbrev}</finalName>
+ <transformers>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+ <manifestEntries>
+ <Main-Class>${app.main.class}</Main-Class>
+ <!--suppress MavenModelInspection -->
+ <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
+ <!--suppress MavenModelInspection -->
+ <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
+ </manifestEntries>
+ </transformer>
+ </transformers>
+ <filters>
+ </filters>
+ </configuration>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+</project>
\ No newline at end of file
diff --git a/public/biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala b/public/biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
new file mode 100644
index 0000000000000000000000000000000000000000..f3eae932c03aee22aa3867c243d93eeda479dcc5
--- /dev/null
+++ b/public/biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
@@ -0,0 +1,48 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet
+
+import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
+
+object BiopetToolsExecutable extends BiopetExecutable {
+
+ def pipelines: List[MainCommand] = Nil
+
+ def tools: List[MainCommand] = List(
+ nl.lumc.sasc.biopet.tools.MergeTables,
+ nl.lumc.sasc.biopet.tools.WipeReads,
+ nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
+ nl.lumc.sasc.biopet.tools.FastqSync,
+ nl.lumc.sasc.biopet.tools.BiopetFlagstat,
+ nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
+ nl.lumc.sasc.biopet.tools.VcfToTsv,
+ nl.lumc.sasc.biopet.tools.VcfFilter,
+ nl.lumc.sasc.biopet.tools.VcfStats,
+ nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
+ nl.lumc.sasc.biopet.tools.MpileupToVcf,
+ nl.lumc.sasc.biopet.tools.FastqSplitter,
+ nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
+ nl.lumc.sasc.biopet.tools.SageCountFastq,
+ nl.lumc.sasc.biopet.tools.SageCreateLibrary,
+ nl.lumc.sasc.biopet.tools.SageCreateTagCounts,
+ nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
+ nl.lumc.sasc.biopet.tools.MergeAlleles,
+ nl.lumc.sasc.biopet.tools.SamplesTsvToJson,
+ nl.lumc.sasc.biopet.tools.SeqStat,
+ nl.lumc.sasc.biopet.tools.VepNormalizer,
+ nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
+ nl.lumc.sasc.biopet.tools.VcfWithVcf)
+}
diff --git a/public/biopet-tools/pom.xml b/public/biopet-tools/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..40bd255bd5730293f1973be9a3db1e49fe909d08
--- /dev/null
+++ b/public/biopet-tools/pom.xml
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <parent>
+ <artifactId>Biopet</artifactId>
+ <groupId>nl.lumc.sasc</groupId>
+ <version>0.5.0-SNAPSHOT</version>
+ <relativePath>../</relativePath>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+
+ <artifactId>BiopetTools</artifactId>
+
+ <repositories>
+ <repository>
+ <id>biojava-maven-repo</id>
+ <name>BioJava repository</name>
+ <url>http://www.biojava.org/download/maven/</url>
+ </repository>
+ </repositories>
+ <dependencies>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>1.9.5</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.10</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetUtils</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.google.guava</groupId>
+ <artifactId>guava</artifactId>
+ <version>18.0</version>
+ </dependency>
+ <dependency>
+ <groupId>org.biojava</groupId>
+ <artifactId>biojava3-sequencing</artifactId>
+ <version>3.1.0</version>
+ </dependency>
+ </dependencies>
+</project>
\ No newline at end of file
diff --git a/public/biopet-tools/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R b/public/biopet-tools/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
new file mode 100644
index 0000000000000000000000000000000000000000..7f7237e90f6593e3d6cf110da005cd89c154d466
--- /dev/null
+++ b/public/biopet-tools/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R
@@ -0,0 +1,35 @@
+library('gplots')
+library('RColorBrewer')
+
+args <- commandArgs(TRUE)
+inputArg <- args[1]
+outputArg <- args[2]
+outputArgClustering <- args[3]
+outputArgDendrogram <- args[4]
+
+
+heat<-read.table(inputArg, header = 1, sep= '\t', stringsAsFactors = F)
+#heat[heat==1] <- NA
+rownames(heat) <- heat[,1]
+heat<- heat[,-1]
+heat<- as.matrix(heat)
+
+colNumber <- 50
+col <- rev(colorRampPalette(brewer.pal(11, "Spectral"))(colNumber))
+for (i in (colNumber+1):(colNumber+round((dist(range(heat)) - dist(range(heat[heat < 1]))) / dist(range(heat[heat < 1])) * colNumber))) {
+ col[i] <- col[colNumber]
+}
+col[length(col)] <- "#00FF00"
+
+png(file = outputArg, width = 1200, height = 1200)
+heatmap.2(heat, trace = 'none', col = col, Colv=NA, Rowv=NA, dendrogram="none", margins = c(12, 12), na.color="#00FF00")
+dev.off()
+
+hc <- hclust(d = dist(heat))
+png(file = outputArgDendrogram, width = 1200, height = 1200)
+plot(as.dendrogram(hc), horiz=TRUE, asp=0.02)
+dev.off()
+
+png(file = outputArgClustering, width = 1200, height = 1200)
+heatmap.2(heat, trace = 'none', col = col, Colv="Rowv", dendrogram="row",margins = c(12, 12), na.color="#00FF00")
+dev.off()
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
index af3294c47a58f16ccf8d8f618ced98bbc5d0077b..5eedb3db7c718a6b5293fab25bff182c629e3909 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
@@ -20,16 +20,12 @@ import java.io.File
import htsjdk.variant.variantcontext.VariantContextBuilder
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf.{ VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine }
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.utils.ToolCommand
import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
import scala.collection.JavaConversions._
-import scala.collection.mutable
-import scala.io.Source
-class AnnotateVcfWithBed {
- // TODO: Queue wrapper
-}
+// TODO: Queue wrapper
/**
* This a tools to annotate a vcf file with values from a bed file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
similarity index 80%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index 33c26353d93c44b80c9f8750de4695eb60e4592a..2ad247900d7a1537e93c3f20b039cf1962d1fa42 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -21,62 +21,12 @@ import htsjdk.samtools.SamReaderFactory
import htsjdk.samtools.reference.IndexedFastaSequenceFile
import htsjdk.variant.variantcontext.VariantContext
import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ Reference, ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.utils.ToolCommand
import nl.lumc.sasc.biopet.utils.VcfUtils._
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import scala.collection.mutable.ListBuffer
-class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input vcf file", required = false)
- var inputVcf: File = _
-
- @Input(doc = "Bam File", required = false)
- var bamFile: File = _
-
- @Input(doc = "reference", required = false)
- var reference: File = _
-
- @Output(doc = "Output fasta, variants only", required = false)
- var outputVariants: File = _
-
- @Output(doc = "Output fasta, variants only", required = false)
- var outputConsensus: File = _
-
- @Output(doc = "Output fasta, variants only", required = false)
- var outputConsensusVariants: File = _
-
- var snpsOnly: Boolean = config("snps_only", default = false)
- var sampleName: String = _
- var minAD: Int = config("min_ad", default = 8)
- var minDepth: Int = config("min_depth", default = 8)
- var outputName: String = _
-
- override def defaultCoreMemory = 4.0
-
- override def beforeGraph(): Unit = {
- super.beforeGraph()
- reference = referenceFasta()
- }
-
- override def commandLine = super.commandLine +
- optional("--inputVcf", inputVcf) +
- optional("--bamFile", bamFile) +
- optional("--outputVariants", outputVariants) +
- optional("--outputConsensus", outputConsensus) +
- optional("--outputConsensusVariants", outputConsensusVariants) +
- conditional(snpsOnly, "--snpsOnly") +
- optional("--sampleName", sampleName) +
- required("--outputName", outputName) +
- optional("--minAD", minAD) +
- optional("--minDepth", minDepth) +
- optional("--reference", reference)
-}
-
object BastyGenerateFasta extends ToolCommand {
case class Args(inputVcf: File = null,
outputVariants: File = null,
@@ -155,7 +105,7 @@ object BastyGenerateFasta extends ToolCommand {
}
}
- protected var cmdArgs: Args = _
+ protected implicit var cmdArgs: Args = _
private val chunkSize = 100000
/**
@@ -165,11 +115,18 @@ object BastyGenerateFasta extends ToolCommand {
val argsParser = new OptParser
cmdArgs = argsParser.parse(args, Args()) getOrElse sys.exit(1)
- if (cmdArgs.outputVariants != null) writeVariantsOnly()
- if (cmdArgs.outputConsensus != null || cmdArgs.outputConsensusVariants != null) writeConsensus()
+ if (cmdArgs.outputVariants != null) {
+ writeVariantsOnly()
+ }
+ if (cmdArgs.outputConsensus != null || cmdArgs.outputConsensusVariants != null) {
+ writeConsensus()
+ }
+
+ //FIXME: what to do if outputcConsensus is set, but not outputConsensusVariants (and vice versa)?
}
protected def writeConsensus() {
+ //FIXME: preferably split this up in functions, so that they can be unit tested
val referenceFile = new IndexedFastaSequenceFile(cmdArgs.reference)
val referenceDict = referenceFile.getSequenceDictionary
@@ -253,7 +210,7 @@ object BastyGenerateFasta extends ToolCommand {
}
}
- protected def writeVariantsOnly() {
+ protected[tools] def writeVariantsOnly() {
val writer = new PrintWriter(cmdArgs.outputVariants)
writer.println(">" + cmdArgs.outputName)
val vcfReader = new VCFFileReader(cmdArgs.inputVcf, false)
@@ -265,17 +222,34 @@ object BastyGenerateFasta extends ToolCommand {
vcfReader.close()
}
- protected def getMaxAllele(vcfRecord: VariantContext): String = {
+ // TODO: what does this do?
+ // Seems to me it finds the allele in a sample with the highest AD value
+ // if this allele is shorter than the largest allele, it will append '-' to the string
+ protected[tools] def getMaxAllele(vcfRecord: VariantContext)(implicit cmdArgs: Args): String = {
val maxSize = getLongestAllele(vcfRecord).getBases.length
- if (cmdArgs.sampleName == null) return fillAllele(vcfRecord.getReference.getBaseString, maxSize)
+ if (cmdArgs.sampleName == null) {
+ return fillAllele(vcfRecord.getReference.getBaseString, maxSize)
+ }
val genotype = vcfRecord.getGenotype(cmdArgs.sampleName)
- if (genotype == null) return fillAllele("", maxSize)
+
+ if (genotype == null) {
+ return fillAllele("", maxSize)
+ }
+
val AD = if (genotype.hasAD) genotype.getAD else Array.fill(vcfRecord.getAlleles.size())(cmdArgs.minAD)
- if (AD == null) return fillAllele("", maxSize)
+
+ if (AD == null) {
+ return fillAllele("", maxSize)
+ }
+
val maxADid = AD.zipWithIndex.maxBy(_._1)._2
- if (AD(maxADid) < cmdArgs.minAD) return fillAllele("", maxSize)
+
+ if (AD(maxADid) < cmdArgs.minAD) {
+ return fillAllele("", maxSize)
+ }
+
fillAllele(vcfRecord.getAlleles()(maxADid).getBaseString, maxSize)
}
-}
\ No newline at end of file
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
similarity index 75%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
index 37f6e5ddcbc570dda20925fc517df0f38ae30391..4a08e55eca849eb40e0de7867f9504e83ac26cdb 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
@@ -18,43 +18,15 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.config.Configurable
import scala.io.Source
-/**
- * @deprecated Use picard.util.BedToIntervalList instead
- */
-class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input Bed file", required = true)
- var input: File = _
-
- @Input(doc = "Bam File", required = true)
- var bamFile: File = _
-
- @Output(doc = "Output interval list", required = true)
- var output: File = _
-
- override def defaultCoreMemory = 1.0
-
- override def commandLine = super.commandLine + required("-I", input) + required("-b", bamFile) + required("-o", output)
-}
-
/**
* @deprecated Use picard.util.BedToIntervalList instead
*/
object BedToInterval extends ToolCommand {
- def apply(root: Configurable, inputBed: File, inputBam: File, output: File): BedToInterval = {
- val bedToInterval = new BedToInterval(root)
- bedToInterval.input = inputBed
- bedToInterval.bamFile = inputBam
- bedToInterval.output = output
- bedToInterval
- }
case class Args(inputFile: File = null, outputFile: File = null, bamFile: File = null) extends AbstractArgs
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
similarity index 75%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
index 2d3fb2b1cadc16a9f0d9db21c261654dacd9d0a9..b9ef718165ff3a7f2b67853c83c3e7d0fbbbe297 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
@@ -17,29 +17,11 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
-import scala.collection.{ mutable, SortedMap }
+import scala.collection.{ SortedMap, mutable }
import scala.io.Source
-class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input fasta", shortName = "input", required = true)
- var input: File = _
-
- @Output(doc = "Output tag library", shortName = "output", required = true)
- var output: File = _
-
- override def defaultCoreMemory = 3.0
-
- override def commandLine = super.commandLine +
- required("-I", input) +
- required("-o", output)
-}
-
object BedtoolsCoverageToCounts extends ToolCommand {
case class Args(input: File = null, output: File = null) extends AbstractArgs
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
similarity index 86%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
index 963d73ebc3625292377bcbf7b3d725fbb47c9e3b..4d98bda24b5c4eb1072cd5d1739efbf242d4a1bf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
@@ -18,55 +18,25 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.{ ToolCommand, ConfigUtils }
import scala.collection.JavaConversions._
import scala.collection.mutable
-class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input bam", shortName = "input", required = true)
- var input: File = _
-
- @Output(doc = "Output flagstat", shortName = "output", required = true)
- var output: File = _
-
- @Output(doc = "summary output file", shortName = "output", required = false)
- var summaryFile: File = _
-
- override def defaultCoreMemory = 6.0
-
- override def commandLine = super.commandLine + required("-I", input) + required("-s", summaryFile) + " > " + required(output)
-
- def summaryFiles: Map[String, File] = Map()
-
- def summaryStats: Map[String, Any] = {
- ConfigUtils.fileToConfigMap(summaryFile)
- }
-}
-
object BiopetFlagstat extends ToolCommand {
- import scala.collection.mutable.Map
-
- def apply(root: Configurable, input: File, outputDir: File): BiopetFlagstat = {
- val flagstat = new BiopetFlagstat(root)
- flagstat.input = input
- flagstat.output = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat")
- flagstat.summaryFile = new File(outputDir, input.getName.stripSuffix(".bam") + ".biopetflagstat.json")
- flagstat
- }
- case class Args(inputFile: File = null, summaryFile: Option[File] = None, region: Option[String] = None) extends AbstractArgs
+ case class Args(inputFile: File = null,
+ outputFile: Option[File] = None,
+ summaryFile: Option[File] = None,
+ region: Option[String] = None) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
} text "input bam file"
+ opt[File]('o', "outputFile") valueName "<file>" action { (x, c) =>
+ c.copy(outputFile = Some(x))
+ } text "output file"
opt[File]('s', "summaryFile") valueName "<file>" action { (x, c) =>
c.copy(summaryFile = Some(x))
} text "summary output file"
@@ -151,7 +121,14 @@ object BiopetFlagstat extends ToolCommand {
writer.close()
}
- println(flagstatCollector.report)
+ commandArgs.outputFile match {
+ case Some(file) => {
+ val writer = new PrintWriter(file)
+ writer.println(flagstatCollector.report)
+ writer.close()
+ }
+ case _ => println(flagstatCollector.report)
+ }
}
class FlagstatCollector {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
index 2797ffc2de25d6045f7717947149cd3900437ced..141633c5358a21c931555d5efbd18c615b7c6f77 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
@@ -21,7 +21,7 @@ import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReader, SamReaderFactory }
import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf.{ VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine }
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.JavaConversions._
import scala.collection.mutable
@@ -116,7 +116,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
}
val counts = for (samRecord <- bamIter if !filterRead(samRecord)) {
- checkAlles(samRecord, vcfRecord) match {
+ checkAlleles(samRecord, vcfRecord) match {
case Some(a) => if (countReports(sample).aCounts.contains(a)) countReports(sample).aCounts(a) += 1
else countReports(sample).aCounts += (a -> 1)
case _ => countReports(sample).notFound += 1
@@ -142,7 +142,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
writer.close()
}
- def checkAlles(samRecord: SAMRecord, vcfRecord: VariantContext): Option[String] = {
+ def checkAlleles(samRecord: SAMRecord, vcfRecord: VariantContext): Option[String] = {
val readStartPos = List.range(0, samRecord.getReadBases.length)
.find(x => samRecord.getReferencePositionAtReadPosition(x + 1) == vcfRecord.getStart) getOrElse { return None }
val readBases = samRecord.getReadBases
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
index 57885eedfa68c7ac2c31312f1579f3b5fcda850b..b02074875b2e27021e123139da7ef42d1bce8700 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala
@@ -20,7 +20,7 @@ import java.io.File
import htsjdk.samtools.{ QueryInterval, SamReaderFactory, ValidationStringency }
import htsjdk.samtools.fastq.{ BasicFastqWriter, FastqReader, FastqRecord }
import htsjdk.samtools.util.Interval
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.JavaConverters._
import scala.collection.mutable.{ Set => MSet }
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
similarity index 74%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
index 0639841bf0e7db21337fa268f446ee3c42117e97..46a4abd0cac604dedc239845565f5d1acdd85b72 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
@@ -18,30 +18,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-
-/**
- * Queue extension for the FastqSplitter
- * @param root Parent object
- */
-class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input fastq", shortName = "input", required = true)
- var input: File = _
-
- @Output(doc = "Output fastq files", shortName = "output", required = true)
- var output: List[File] = Nil
-
- override def defaultCoreMemory = 4.0
-
- /** * Generate command to execute */
- override def commandLine = super.commandLine +
- required("-I", input) +
- repeat("-o", output)
-}
+import nl.lumc.sasc.biopet.utils.ToolCommand
object FastqSplitter extends ToolCommand {
@@ -55,10 +32,10 @@ object FastqSplitter extends ToolCommand {
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
- } text "out is a required file property"
+ } text "Path to input file"
opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) =>
c.copy(outputFile = x :: c.outputFile)
- } text "out is a required file property"
+ } text "Path to output file"
}
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
similarity index 71%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index 9c320e4143dfae64108ae0c0e90a1339681b85a6..d4e6996de89b9a62a3b35f9ea894907882b4484f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -18,88 +18,10 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.annotation.tailrec
import scala.collection.JavaConverters._
-import scala.io.Source
-import scala.util.matching.Regex
-
-/**
- * FastqSync function class for usage in Biopet pipelines
- *
- * @param root Configuration object for the pipeline
- */
-class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summarizable {
-
- javaMainClass = getClass.getName
-
- @Input(doc = "Original FASTQ file (read 1 or 2)", shortName = "r", required = true)
- var refFastq: File = null
-
- @Input(doc = "Input read 1 FASTQ file", shortName = "i", required = true)
- var inputFastq1: File = null
-
- @Input(doc = "Input read 2 FASTQ file", shortName = "j", required = true)
- var inputFastq2: File = null
-
- @Output(doc = "Output read 1 FASTQ file", shortName = "o", required = true)
- var outputFastq1: File = null
-
- @Output(doc = "Output read 2 FASTQ file", shortName = "p", required = true)
- var outputFastq2: File = null
-
- @Output(doc = "Sync statistics", required = true)
- var outputStats: File = null
-
- override def defaultCoreMemory = 4.0
-
- // executed command line
- override def commandLine =
- super.commandLine +
- required("-r", refFastq) +
- required("-i", inputFastq1) +
- required("-j", inputFastq2) +
- required("-o", outputFastq1) +
- required("-p", outputFastq2) + " > " +
- required(outputStats)
-
- def summaryFiles: Map[String, File] = Map()
-
- def summaryStats: Map[String, Any] = {
- val regex = new Regex("""Filtered (\d*) reads from first read file.
- |Filtered (\d*) reads from second read file.
- |Synced read files contain (\d*) reads.""".stripMargin,
- "R1", "R2", "RL")
-
- val (countFilteredR1, countFilteredR2, countRLeft) =
- if (outputStats.exists) {
- val text = Source
- .fromFile(outputStats)
- .getLines()
- .mkString("\n")
- regex.findFirstMatchIn(text) match {
- case None => (0, 0, 0)
- case Some(rmatch) => (rmatch.group("R1").toInt, rmatch.group("R2").toInt, rmatch.group("RL").toInt)
- }
- } else (0, 0, 0)
-
- Map("num_reads_discarded_R1" -> countFilteredR1,
- "num_reads_discarded_R2" -> countFilteredR2,
- "num_reads_kept" -> countRLeft
- )
- }
-
- override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
- (v1, v2) match {
- case (v1: Int, v2: Int) => v1 + v2
- case _ => v1
- }
- }
-}
object FastqSync extends ToolCommand {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
similarity index 81%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
index dafa21f20d18ce0c0e364e17778b3547f0d2ed67..f752e3be6863928122bf233b9b911b2d50b8a432 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
@@ -15,24 +15,29 @@
*/
package nl.lumc.sasc.biopet.tools
-import java.io.File
+import java.io.{ PrintWriter, File }
import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReaderFactory, ValidationStringency }
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.JavaConversions._
import scala.io.Source
object FindRepeatsPacBio extends ToolCommand {
- case class Args(inputBam: File = null, inputBed: File = null) extends AbstractArgs
+ case class Args(inputBam: File = null,
+ outputFile: Option[File] = None,
+ inputBed: File = null) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "inputBam") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputBam = x)
- }
+ } text "Path to input file"
+ opt[File]('o', "outputFile") maxOccurs 1 valueName "<file>" action { (x, c) =>
+ c.copy(outputFile = Some(x))
+ } text "Path to input file"
opt[File]('b', "inputBed") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputBed = x)
- } text "output file, default to stdout"
+ } text "Path to bed file"
}
/**
@@ -50,7 +55,6 @@ object FindRepeatsPacBio extends ToolCommand {
val header = List("chr", "startPos", "stopPos", "Repeat_seq", "repeatLength",
"original_Repeat_readLength", "Calculated_repeat_readLength",
"minLength", "maxLength", "inserts", "deletions", "notSpan")
- println(header.mkString("\t"))
for (
bedLine <- Source.fromFile(commandArgs.inputBed).getLines();
@@ -84,9 +88,21 @@ object FindRepeatsPacBio extends ToolCommand {
if (length < minLength || minLength == -1) minLength = length
}
}
- println(List(chr, startPos, stopPos, typeRepeat, repeatLength, oriRepeatLength, calcRepeatLength.mkString(","), minLength,
- maxLength, inserts.mkString("/"), deletions.mkString("/"), notSpan).mkString("\t"))
bamIter.close()
+ commandArgs.outputFile match {
+ case Some(file) => {
+ val writer = new PrintWriter(file)
+ writer.println(header.mkString("\t"))
+ writer.println(List(chr, startPos, stopPos, typeRepeat, repeatLength, oriRepeatLength, calcRepeatLength.mkString(","), minLength,
+ maxLength, inserts.mkString("/"), deletions.mkString("/"), notSpan).mkString("\t"))
+ writer.close()
+ }
+ case _ => {
+ println(header.mkString("\t"))
+ println(List(chr, startPos, stopPos, typeRepeat, repeatLength, oriRepeatLength, calcRepeatLength.mkString(","), minLength,
+ maxLength, inserts.mkString("/"), deletions.mkString("/"), notSpan).mkString("\t"))
+ }
+ }
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
similarity index 75%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index 8a5b05f6e00575090f687436b7bd348ba34cb6a2..02f4b4709398e244a40ba13139993d2230d54fd3 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -18,52 +18,16 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.samtools.reference.FastaSequenceFile
-import htsjdk.variant.variantcontext.{ Allele, VariantContext, VariantContextBuilder }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
+import htsjdk.variant.variantcontext.{ Allele, VariantContext, VariantContextBuilder }
import htsjdk.variant.vcf.{ VCFFileReader, VCFHeader }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.config.Configurable
import scala.collection.JavaConversions._
-import scala.collection.{ mutable, SortedMap }
-import scala.collection.mutable.{ Map, Set }
-
-class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input vcf files", shortName = "input", required = true)
- var input: List[File] = Nil
-
- @Output(doc = "Output vcf file", shortName = "output", required = true)
- var output: File = _
-
- @Output(doc = "Output vcf file index", shortName = "output", required = true)
- private var outputIndex: File = _
-
- var reference: File = config("reference")
-
- override def defaultCoreMemory = 1.0
-
- override def beforeGraph() {
- super.beforeGraph()
- if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
- if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
- }
-
- override def commandLine = super.commandLine +
- repeat("-I", input) +
- required("-o", output) +
- required("-R", reference)
-}
+import scala.collection.{ SortedMap, mutable }
object MergeAlleles extends ToolCommand {
- def apply(root: Configurable, input: List[File], output: File): MergeAlleles = {
- val mergeAlleles = new MergeAlleles(root)
- mergeAlleles.input = input
- mergeAlleles.output = output
- mergeAlleles
- }
case class Args(inputFiles: List[File] = Nil, outputFile: File = null, reference: File = null) extends AbstractArgs
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
similarity index 80%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
index e587df068766514e05bfa7ea17ca626a733f03bb..680cba33443e7efbcda4e2acb5b42809a12b3f5c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
@@ -17,68 +17,11 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ BufferedWriter, File, FileWriter, OutputStreamWriter }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.mutable.{ Set => MutSet }
import scala.io.{ BufferedSource, Source }
-/**
- * Biopet wrapper for the [[MergeTables]] command line tool.
- *
- * @param root [[Configurable]] object
- */
-class MergeTables(val root: Configurable) extends ToolCommandFuntion {
-
- javaMainClass = getClass.getName
-
- override def defaultCoreMemory = 6.0
-
- /** List of input tabular files */
- @Input(doc = "Input table files", required = true)
- var inputTables: List[File] = List.empty[File]
-
- /** Output file */
- @Output(doc = "Output merged table", required = true)
- var output: File = null
-
- // TODO: should be List[Int] really
- /** List of column indices to combine to make a unique identifier per row */
- var idColumnIndices: List[String] = config("id_column_indices", default = List("1"))
-
- /** Index of column from each tabular file containing the values to be put in the final merged table */
- var valueColumnIndex: Int = config("value_column_index", default = 2)
-
- /** Name of the identifier column in the output file */
- var idColumnName: Option[String] = config("id_column_name")
-
- /** Common file extension of all input files */
- var fileExtension: Option[String] = config("file_extension")
-
- /** Number of header lines from each input file to ignore */
- var numHeaderLines: Option[Int] = config("num_header_lines")
-
- /** String to use when a value is missing from an input file */
- var fallbackString: Option[String] = config("fallback_string")
-
- /** Column delimiter of each input file (used for splitting into columns */
- var delimiter: Option[String] = config("delimiter")
-
- // executed command line
- override def commandLine =
- super.commandLine +
- required("-i", idColumnIndices.mkString(",")) +
- required("-a", valueColumnIndex) +
- optional("-n", idColumnName) +
- optional("-e", fileExtension) +
- optional("-m", numHeaderLines) +
- optional("-f", fallbackString) +
- optional("-d", delimiter) +
- required("-o", output) +
- required("", repeat(inputTables), escape = false)
-}
-
object MergeTables extends ToolCommand {
/** Type alias for sample name */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
similarity index 75%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index bed6e3b6ec2149f8ac4cc0d80420e02829a170f1..c93eaed3993830d9e1860b827d772b2c925b6983 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -17,77 +17,13 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
-import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ Reference, ToolCommand, ToolCommandFuntion }
-import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
-import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
-import scala.collection.JavaConversions._
import scala.collection.mutable
import scala.collection.mutable.ArrayBuffer
import scala.io.Source
import scala.math.{ floor, round }
-class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input mpileup file", shortName = "mpileup", required = false)
- var inputMpileup: File = _
-
- @Input(doc = "Input bam file", shortName = "bam", required = false)
- var inputBam: File = _
-
- @Output(doc = "Output tag library", shortName = "output", required = true)
- var output: File = _
-
- var minDP: Option[Int] = config("min_dp")
- var minAP: Option[Int] = config("min_ap")
- var homoFraction: Option[Double] = config("homoFraction")
- var ploidy: Option[Int] = config("ploidy")
- var sample: String = _
- var reference: String = _
-
- override def defaultCoreMemory = 3.0
-
- override def defaults = ConfigUtils.mergeMaps(Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1)),
- super.defaults)
-
- override def beforeGraph() {
- super.beforeGraph()
- reference = referenceFasta().getAbsolutePath
- val samtoolsMpileup = new SamtoolsMpileup(this)
- }
-
- override def beforeCmd(): Unit = {
- if (sample == null && inputBam.exists()) {
- val inputSam = SamReaderFactory.makeDefault.open(inputBam)
- val readGroups = inputSam.getFileHeader.getReadGroups
- val samples = readGroups.map(readGroup => readGroup.getSample).distinct
- sample = samples.head
- inputSam.close()
- }
- }
-
- override def commandLine = {
- (if (inputMpileup == null) {
- val samtoolsMpileup = new SamtoolsMpileup(this)
- samtoolsMpileup.reference = referenceFasta()
- samtoolsMpileup.input = List(inputBam)
- samtoolsMpileup.cmdPipe + " | "
- } else "") +
- super.commandLine +
- required("-o", output) +
- optional("--minDP", minDP) +
- optional("--minAP", minAP) +
- optional("--homoFraction", homoFraction) +
- optional("--ploidy", ploidy) +
- required("--sample", sample) +
- (if (inputBam == null) required("-I", inputMpileup) else "")
- }
-}
-
object MpileupToVcf extends ToolCommand {
case class Args(input: File = null, output: File = null, sample: String = null, minDP: Int = 8, minAP: Int = 2,
homoFraction: Double = 0.8, ploidy: Int = 2) extends AbstractArgs
@@ -122,8 +58,6 @@ object MpileupToVcf extends ToolCommand {
def main(args: Array[String]): Unit = {
val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
-
- import scala.collection.mutable.Map
if (commandArgs.input != null && !commandArgs.input.exists) throw new IllegalStateException("Input file does not exist")
val writer = new PrintWriter(commandArgs.output)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
similarity index 66%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
index cc4305d4b1708206c1d47d0dd60419cedd0ba7cf..a5040a24f735e88d0c0877b7e2e0923c1e5de2c8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
@@ -18,54 +18,10 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
-
-/**
- * Queue class for PrefixFastq tool
- *
- * Created by pjvan_thof on 1/13/15.
- */
-class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- override def defaultCoreMemory = 1.0
-
- @Input(doc = "Input fastq", shortName = "I", required = true)
- var inputFastq: File = _
-
- @Output(doc = "Output fastq", shortName = "o", required = true)
- var outputFastq: File = _
-
- @Argument(doc = "Prefix seq", required = true)
- var prefixSeq: String = _
-
- /**
- * Creates command to execute extension
- * @return
- */
- override def commandLine = super.commandLine +
- required("-i", inputFastq) +
- required("-o", outputFastq) +
- optional("-s", prefixSeq)
-}
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.config.Configurable
object PrefixFastq extends ToolCommand {
- /**
- * Create a PrefixFastq class object with a sufix ".prefix.fastq" in the output folder
- *
- * @param root parent object
- * @param input input file
- * @param outputDir outputFolder
- * @return PrefixFastq class object
- */
- def apply(root: Configurable, input: File, outputDir: String): PrefixFastq = {
- val prefixFastq = new PrefixFastq(root)
- prefixFastq.inputFastq = input
- prefixFastq.outputFastq = new File(outputDir, input.getName + ".prefix.fastq")
- prefixFastq
- }
/**
* Args for commandline program
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
index 4766f31d5fd78af68ece6fcb8a5a410cfb4ae951..bdfb0be7f8e51495fed176ac7ab386104a04948e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
@@ -19,8 +19,8 @@ import java.io.{ PrintWriter, InputStream, File }
import java.util
import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.core.ToolCommand
-import nl.lumc.sasc.biopet.extensions.rscript.ScatterPlot
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.rscript.ScatterPlot
import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
import scala.collection.JavaConversions._
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
similarity index 73%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
index c24134181ab3cc6d3cac9c2bd5576f643b51f688..2049a337670655d56c0846e3e64eb6274d6f8d7a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
@@ -17,29 +17,10 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ File, FileReader, PrintWriter }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.biojava3.sequencing.io.fastq.{ Fastq, SangerFastqReader, StreamListener }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import org.biojava3.sequencing.io.fastq.{ Fastq, StreamListener, SangerFastqReader }
-import scala.collection.{ mutable, SortedMap }
-import scala.collection.mutable.Map
-
-class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input fasta", shortName = "input", required = true)
- var input: File = _
-
- @Output(doc = "Output tag library", shortName = "output", required = true)
- var output: File = _
-
- override def defaultCoreMemory = 3.0
-
- override def commandLine = super.commandLine +
- required("-I", input) +
- required("-o", output)
-}
+import scala.collection.{ SortedMap, mutable }
object SageCountFastq extends ToolCommand {
case class Args(input: File = null, output: File = null) extends AbstractArgs
@@ -73,7 +54,7 @@ object SageCountFastq extends ToolCommand {
if (counts.contains(seq)) counts(seq) += 1
else counts += (seq -> 1)
count += 1
- if (count % 1000000 == 0) System.err.println(count + " sequences done")
+ if (count % 1000000 == 0) logger.info(count + " sequences done")
}
})
logger.info(count + " sequences done")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
similarity index 72%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
index 674717fca9e51d3b76a6e8991ad69f6de03ebb0d..f5ffa5e5a43e63c95d6610ca9e58c1170ae44369 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
@@ -17,48 +17,13 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.utils.ToolCommand
import org.biojava3.core.sequence.DNASequence
import org.biojava3.core.sequence.io.FastaReaderHelper
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import scala.collection.JavaConversions._
-import scala.collection.{ mutable, SortedMap }
-import scala.collection.mutable.{ Map, Set }
+import scala.collection.{ SortedMap, mutable }
import scala.util.matching.Regex
-
-class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input fasta", shortName = "input", required = true)
- var input: File = _
-
- @Output(doc = "Output tag library", shortName = "output", required = true)
- var output: File = _
-
- @Output(doc = "Output no tags", shortName = "noTagsOutput", required = false)
- var noTagsOutput: File = _
-
- @Output(doc = "Output no anti tags library", shortName = "noAntiTagsOutput", required = false)
- var noAntiTagsOutput: File = _
-
- @Output(doc = "Output file all genes", shortName = "allGenes", required = false)
- var allGenesOutput: File = _
-
- var tag: String = config("tag", default = "CATG")
- var length: Option[Int] = config("length", default = 17)
-
- override def defaultCoreMemory = 3.0
-
- override def commandLine = super.commandLine +
- required("-I", input) +
- optional("--tag", tag) +
- optional("--length", length) +
- optional("--noTagsOutput", noTagsOutput) +
- optional("--noAntiTagsOutput", noAntiTagsOutput) +
- required("-o", output)
-}
+import scala.collection.JavaConversions._
object SageCreateLibrary extends ToolCommand {
case class Args(input: File = null, tag: String = "CATG", length: Int = 17, output: File = null, noTagsOutput: File = null,
@@ -77,10 +42,10 @@ object SageCreateLibrary extends ToolCommand {
opt[Int]("length") required () unbounded () action { (x, c) =>
c.copy(length = x)
}
- opt[File]("noTagsOutput") required () unbounded () valueName "<file>" action { (x, c) =>
+ opt[File]("noTagsOutput") unbounded () valueName "<file>" action { (x, c) =>
c.copy(noTagsOutput = x)
}
- opt[File]("noAntiTagsOutput") required () unbounded () valueName "<file>" action { (x, c) =>
+ opt[File]("noAntiTagsOutput") unbounded () valueName "<file>" action { (x, c) =>
c.copy(noAntiTagsOutput = x)
}
opt[File]("allGenesOutput") unbounded () valueName "<file>" action { (x, c) =>
@@ -88,8 +53,7 @@ object SageCreateLibrary extends ToolCommand {
}
}
- var tagRegex: Regex = null
- var geneRegex = """ENSG[0-9]{11}""".r
+ val geneRegex = """ENSG[0-9]{11}""".r
val tagGenesMap: mutable.Map[String, TagGenes] = mutable.Map()
@@ -114,23 +78,24 @@ object SageCreateLibrary extends ToolCommand {
if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
- tagRegex = (commandArgs.tag + "[CATG]{" + commandArgs.length + "}").r
+ val tagRegex = (commandArgs.tag + "[CATG]{" + commandArgs.length + "}").r
var count = 0
- System.err.println("Reading fasta file")
+ logger.info("Reading fasta file")
val reader = FastaReaderHelper.readFastaDNASequence(commandArgs.input)
- System.err.println("Finding tags")
+ logger.info("Finding tags")
for ((name, seq) <- reader) {
- getTags(name, seq)
+ val result = getTags(name, seq, tagRegex)
+ addTagresultToTaglib(name, result)
count += 1
- if (count % 10000 == 0) System.err.println(count + " transcripts done")
+ if (count % 10000 == 0) logger.info(count + " transcripts done")
}
- System.err.println(count + " transcripts done")
+ logger.info(count + " transcripts done")
- System.err.println("Start sorting tags")
+ logger.info("Start sorting tags")
val tagGenesMapSorted: SortedMap[String, TagGenes] = SortedMap(tagGenesMap.toArray: _*)
- System.err.println("Writting output files")
+ logger.info("Writting output files")
val writer = new PrintWriter(commandArgs.output)
writer.println("#tag\tfirstTag\tAllTags\tFirstAntiTag\tAllAntiTags")
for ((tag, genes) <- tagGenesMapSorted) {
@@ -167,7 +132,7 @@ object SageCreateLibrary extends ToolCommand {
}
}
- def addTagresultToTaglib(name: String, tagResult: TagResult) {
+ private def addTagresultToTaglib(name: String, tagResult: TagResult) {
val id = name.split(" ").head //.stripPrefix("hg19_ensGene_")
val geneID = geneRegex.findFirstIn(name).getOrElse("unknown_gene")
allGenes.add(geneID)
@@ -195,15 +160,13 @@ object SageCreateLibrary extends ToolCommand {
}
}
- def getTags(name: String, seq: DNASequence): TagResult = {
+ def getTags(name: String, seq: DNASequence, tagRegex: Regex): TagResult = {
val allTags: List[String] = for (tag <- tagRegex.findAllMatchIn(seq.getSequenceAsString).toList) yield tag.toString()
val firstTag = if (allTags.isEmpty) null else allTags.last
val allAntiTags: List[String] = for (tag <- tagRegex.findAllMatchIn(seq.getReverseComplement.getSequenceAsString).toList) yield tag.toString()
val firstAntiTag = if (allAntiTags.isEmpty) null else allAntiTags.head
val result = new TagResult(firstTag, allTags, firstAntiTag, allAntiTags)
- addTagresultToTaglib(name, result)
-
result
}
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
similarity index 74%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
index 1392dcefefba1b5e28b0eb795c7d460c86a3abf2..9ff037eae73d81cd39345d6028e903af220ae35c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
@@ -17,46 +17,11 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
-import scala.collection.{ mutable, SortedMap }
-import scala.collection.mutable.Map
+import scala.collection.{ SortedMap, mutable }
import scala.io.Source
-class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Raw count file", shortName = "input", required = true)
- var input: File = _
-
- @Input(doc = "tag library", shortName = "taglib", required = true)
- var tagLib: File = _
-
- @Output(doc = "Sense count file", shortName = "sense", required = true)
- var countSense: File = _
-
- @Output(doc = "Sense all coun filet", shortName = "allsense", required = true)
- var countAllSense: File = _
-
- @Output(doc = "AntiSense count file", shortName = "antisense", required = true)
- var countAntiSense: File = _
-
- @Output(doc = "AntiSense all count file", shortName = "allantisense", required = true)
- var countAllAntiSense: File = _
-
- override def defaultCoreMemory = 3.0
-
- override def commandLine = super.commandLine +
- required("-I", input) +
- required("--tagLib", tagLib) +
- optional("--countSense", countSense) +
- optional("--countAllSense", countAllSense) +
- optional("--countAntiSense", countAntiSense) +
- optional("--countAllAntiSense", countAllAntiSense)
-}
-
object SageCreateTagCounts extends ToolCommand {
case class Args(input: File = null, tagLib: File = null, countSense: File = null, countAllSense: File = null,
countAntiSense: File = null, countAllAntiSense: File = null) extends AbstractArgs
@@ -148,9 +113,18 @@ object SageCreateTagCounts extends ToolCommand {
writer.close()
}
}
- writeFile(commandArgs.countSense, senseCounts)
- writeFile(commandArgs.countAllSense, allSenseCounts)
- writeFile(commandArgs.countAntiSense, antiSenseCounts)
- writeFile(commandArgs.countAllAntiSense, allAntiSenseCounts)
+
+ if (commandArgs.countSense != null) {
+ writeFile(commandArgs.countSense, senseCounts)
+ }
+ if (commandArgs.countAllAntiSense != null) {
+ writeFile(commandArgs.countAllAntiSense, allAntiSenseCounts)
+ }
+ if (commandArgs.countAllSense != null) {
+ writeFile(commandArgs.countAllSense, allSenseCounts)
+ }
+ if (commandArgs.countAntiSense != null) {
+ writeFile(commandArgs.countAntiSense, antiSenseCounts)
+ }
}
}
\ No newline at end of file
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
new file mode 100644
index 0000000000000000000000000000000000000000..ff31439d9f0622ef73e3386e207971caa715a607
--- /dev/null
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
@@ -0,0 +1,95 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.tools
+
+import java.io.{ PrintWriter, File }
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils._
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import scala.collection.mutable
+
+import scala.io.Source
+
+/**
+ * This tool can convert a tsv to a json file
+ */
+object SamplesTsvToJson extends ToolCommand {
+ case class Args(inputFiles: List[File] = Nil, outputFile: Option[File] = None) extends AbstractArgs
+
+ class OptParser extends AbstractOptParser {
+ opt[File]('i', "inputFiles") required () unbounded () valueName "<file>" action { (x, c) =>
+ c.copy(inputFiles = x :: c.inputFiles)
+ } text "Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed"
+ opt[File]('o', "outputFile") unbounded () valueName "<file>" action { (x, c) =>
+ c.copy(outputFile = Some(x))
+ }
+ }
+
+ /** Executes SamplesTsvToJson */
+ def main(args: Array[String]): Unit = {
+ val argsParser = new OptParser
+ val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+ val jsonString = stringFromInputs(commandArgs.inputFiles)
+ commandArgs.outputFile match {
+ case Some(file) => {
+ val writer = new PrintWriter(file)
+ writer.println(jsonString)
+ writer.close()
+ }
+ case _ => println(jsonString)
+ }
+ }
+
+ def mapFromFile(inputFile: File): Map[String, Any] = {
+ val reader = Source.fromFile(inputFile)
+ val lines = reader.getLines().toList.filter(!_.isEmpty)
+ val header = lines.head.split("\t")
+ val sampleColumn = header.indexOf("sample")
+ val libraryColumn = header.indexOf("library")
+ if (sampleColumn == -1) throw new IllegalStateException("Sample column does not exist in: " + inputFile)
+
+ val sampleLibCache: mutable.Set[(String, Option[String])] = mutable.Set()
+
+ val librariesValues: List[Map[String, Any]] = for (tsvLine <- lines.tail) yield {
+ val values = tsvLine.split("\t")
+ require(header.length == values.length, "Number of columns is not the same as the header")
+ val sample = values(sampleColumn)
+ val library = if (libraryColumn != -1) Some(values(libraryColumn)) else None
+
+ //FIXME: this is a workaround, should be removed after fixing #180
+ if (sample.head.isDigit || library.forall(_.head.isDigit))
+ throw new IllegalStateException("Sample or library may not start with a number")
+
+ if (sampleLibCache.contains((sample, library)))
+ throw new IllegalStateException(s"Combination of $sample ${library.map("and " + _).getOrElse("")} is found multiple times")
+ else sampleLibCache.add((sample, library))
+ val valuesMap = (for (
+ t <- 0 until values.size if !values(t).isEmpty && t != sampleColumn && t != libraryColumn
+ ) yield header(t) -> values(t)).toMap
+ library match {
+ case Some(lib) => Map("samples" -> Map(sample -> Map("libraries" -> Map(lib -> valuesMap))))
+ case _ => Map("samples" -> Map(sample -> valuesMap))
+ }
+ }
+ librariesValues.foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
+ }
+
+ def stringFromInputs(inputs: List[File]): String = {
+ val map = inputs.map(f => mapFromFile(f)).foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
+ mapToJson(map).spaces2
+ }
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
similarity index 77%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
index 1ec41952922c2058d02f680efb8a14a1757c85a2..74d2512b9e09f40430477ab42afd6410f5582514 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
@@ -15,14 +15,10 @@
*/
package nl.lumc.sasc.biopet.tools
-import java.io.File
+import java.io.{ PrintWriter, File }
import htsjdk.samtools.fastq.{ FastqReader, FastqRecord }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.{ ToolCommand, ConfigUtils }
import scala.collection.JavaConverters._
import scala.collection.immutable.Map
@@ -30,65 +26,9 @@ import scala.collection.mutable
import scala.language.postfixOps
/**
- * Seqstat function class for usage in Biopet pipelines
- *
- * @param root Configuration object for the pipeline
+ * Created by pjvanthof on 11/09/15.
*/
-class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input FASTQ", shortName = "input", required = true)
- var input: File = null
-
- @Output(doc = "Output JSON", shortName = "output", required = true)
- var output: File = null
-
- override def defaultCoreMemory = 2.5
-
- override def commandLine = super.commandLine + required("-i", input) + " > " + required(output)
-
- def summaryStats: Map[String, Any] = {
- val map = ConfigUtils.fileToConfigMap(output)
-
- ConfigUtils.any2map(map.getOrElse("stats", Map()))
- }
-
- def summaryFiles: Map[String, File] = Map()
-
- override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
- (v1, v2) match {
- case (v1: Array[_], v2: Array[_]) => v1.zip(v2).map(v => resolveSummaryConflict(v._1, v._2, key))
- case (v1: List[_], v2: List[_]) => v1.zip(v2).map(v => resolveSummaryConflict(v._1, v._2, key))
- case (v1: Int, v2: Int) if key == "len_min" => if (v1 < v2) v1 else v2
- case (v1: Int, v2: Int) if key == "len_max" => if (v1 > v2) v1 else v2
- case (v1: Int, v2: Int) => v1 + v2
- case (v1: Long, v2: Long) => v1 + v2
- case _ => v1
- }
- }
-}
-
-object FqEncoding extends Enumeration {
- type FqEncoding = Value
- val Sanger = Value(33, "Sanger")
- val Solexa = Value(64, "Solexa")
- val Unknown = Value(0, "Unknown")
-}
-
object SeqStat extends ToolCommand {
- def apply(root: Configurable, input: File, output: File): SeqStat = {
- val seqstat = new SeqStat(root)
- seqstat.input = input
- seqstat.output = new File(output, input.getName.substring(0, input.getName.lastIndexOf(".")) + ".seqstats.json")
- seqstat
- }
-
- def apply(root: Configurable, fastqfile: File, outDir: String): SeqStat = {
- val seqstat = new SeqStat(root)
- seqstat.input = fastqfile
- seqstat.output = new File(outDir, fastqfile.getName.substring(0, fastqfile.getName.lastIndexOf(".")) + ".seqstats.json")
- seqstat
- }
import FqEncoding._
@@ -108,20 +48,23 @@ object SeqStat extends ToolCommand {
private var baseQualHistoMap: mutable.Map[Int, Long] = mutable.Map(0 -> 0)
private var readQualHistoMap: mutable.Map[Int, Long] = mutable.Map(0 -> 0)
- case class Args(fastq: File = new File("")) extends AbstractArgs
+ case class Args(fastq: File = null, outputJson: Option[File] = None) extends AbstractArgs
class OptParser extends AbstractOptParser {
head(
s"""
- |$commandName - Summarize FastQ
+ |$commandName - Summarize FastQ
""".stripMargin)
- opt[File]('i', "fastq") required () valueName "<fastq>" action { (x, c) =>
+ opt[File]('i', "fastq") required () unbounded () valueName "<fastq>" action { (x, c) =>
c.copy(fastq = x)
} validate {
x => if (x.exists) success else failure("FASTQ file not found")
} text "FastQ file to generate stats from"
+ opt[File]('o', "output") unbounded () valueName "<json>" action { (x, c) =>
+ c.copy(outputJson = Some(x))
+ } text "File to write output to, if not supplied output go to stdout"
}
/**
@@ -317,6 +260,21 @@ object SeqStat extends ToolCommand {
))
)
- println(ConfigUtils.mapToJson(report))
+ commandArgs.outputJson match {
+ case Some(file) => {
+ val writer = new PrintWriter(file)
+ writer.println(ConfigUtils.mapToJson(report))
+ writer.close()
+ }
+ case _ => println(ConfigUtils.mapToJson(report))
+ }
}
}
+
+object FqEncoding extends Enumeration {
+ type FqEncoding = Value
+ val Sanger = Value(33, "Sanger")
+ val Solexa = Value(64, "Solexa")
+ val Unknown = Value(0, "Unknown")
+}
+
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
similarity index 73%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
index e68af686fff12423181213c77c0d657e7f85d822..74aad0081a547e9b0a25ab2e86c851dbafd4ba3b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
@@ -2,31 +2,12 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
-import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, ToolCommand }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.ToolCommand
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvanthof on 22/08/15.
*/
-class SquishBed(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input Bed file", required = true)
- var input: File = _
-
- @Output(doc = "Output interval list", required = true)
- var output: File = _
-
- var strandSensitive: Boolean = config("strandSensitive", default = false)
-
- override def commandLine = super.commandLine +
- required("-I", input) +
- required("-o", output) +
- conditional(strandSensitive, "-s")
-}
-
object SquishBed extends ToolCommand {
case class Args(input: File = null,
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
similarity index 53%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
index 398a9b73f733963960f7aa5ee55414a086d6127d..9c4629bd45d0111657f871e9587ed09faa6dd611 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
@@ -15,10 +15,10 @@
*/
package nl.lumc.sasc.biopet.tools
-import java.io.File
+import java.io.{ PrintWriter, File }
-import nl.lumc.sasc.biopet.core.ToolCommand
-import nl.lumc.sasc.biopet.core.summary.Summary
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.summary.Summary
/**
* This is a tools to extract values from a summary to a tsv file
@@ -35,15 +35,27 @@ object SummaryToTsv extends ToolCommand {
opt[File]('s', "summary") required () unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(summary = x)
}
- opt[File]('o', "output") maxOccurs 1 unbounded () valueName "<file>" action { (x, c) =>
+ opt[File]('o', "outputFile") unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(outputFile = Some(x))
}
- opt[String]('p', "path") required () unbounded () valueName "<value>" action { (x, c) =>
+ opt[String]('p', "path") required () unbounded () valueName "<string>" action { (x, c) =>
c.copy(values = c.values ::: x :: Nil)
- }
+ } text
+ """
+ |String that determines the values extracted from the summary. Should be of the format:
+ |<header_name>=<namespace>:<lower_namespace>:<even_lower_namespace>...
+ """.stripMargin
opt[String]('m', "mode") maxOccurs 1 unbounded () valueName "<root|sample|lib>" action { (x, c) =>
c.copy(mode = x)
- }
+ } validate {
+ x => if (Set("root", "sample", "lib").contains(x)) success else failure("Unsupported mode")
+ } text
+ """
+ |Determines on what level to aggregate data.
+ |root: at the root level
+ |sample: at the sample level
+ |lib: at the library level
+ """.stripMargin
}
@@ -56,14 +68,23 @@ object SummaryToTsv extends ToolCommand {
val paths = cmdArgs.values.map(x => {
val split = x.split("=", 2)
split(0) -> split(1).split(":")
- })
+ }).toMap
- val values = fetchValues(summary, paths.toMap, sample = cmdArgs.mode == "sample", lib = cmdArgs.mode == "lib")
+ val values = fetchValues(summary, paths, sample = cmdArgs.mode == "sample", lib = cmdArgs.mode == "lib")
- println(paths.map(_._1).mkString("\t", "\t", ""))
-
- for (lineId <- values.head._2.keys) {
- println(paths.map(x => values(x._1)(lineId).getOrElse("")).mkString(lineId + "\t", "\t", ""))
+ cmdArgs.outputFile match {
+ case Some(file) => {
+ val writer = new PrintWriter(file)
+ writer.println(createHeader(paths))
+ for (lineId <- values.head._2.keys)
+ writer.println(createLine(paths, values, lineId))
+ writer.close()
+ }
+ case _ => {
+ println(createHeader(paths))
+ for (lineId <- values.head._2.keys)
+ println(createLine(paths, values, lineId))
+ }
}
}
@@ -71,9 +92,19 @@ object SummaryToTsv extends ToolCommand {
sample: Boolean = false,
lib: Boolean = false) = {
for ((name, path) <- paths) yield name -> {
- if (lib) summary.getLibraryValues(path: _*).map(a => (a._1._1 + "-" + a._1._2) -> a._2)
- else if (sample) summary.getSampleValues(path: _*)
+ if (lib) {
+ summary.getLibraryValues(path: _*).map(a => (a._1._1 + "-" + a._1._2) -> a._2)
+ } else if (sample) summary.getSampleValues(path: _*)
else Map("value" -> summary.getValue(path: _*))
}
}
+
+ def createHeader(paths: Map[String, Array[String]]): String = {
+ paths.map(_._1).mkString("\t", "\t", "")
+ }
+
+ def createLine(paths: Map[String, Array[String]],
+ values: Map[String, Map[String, Option[Any]]], lineId: String): String = {
+ paths.map(x => values(x._1)(lineId).getOrElse("")).mkString(lineId + "\t", "\t", "")
+ }
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
similarity index 91%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index 981203de4652d72e16b5a0b0018d05679943b984..2799fa38b78b6d2acb123b80d5ae5a3bdde3bf3a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
@@ -20,43 +20,15 @@ import java.io.File
import htsjdk.variant.variantcontext.{ GenotypeType, VariantContext }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.config.Configurable
import scala.collection.JavaConversions._
import scala.io.Source
-class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input vcf", shortName = "I", required = true)
- var inputVcf: File = _
-
- @Output(doc = "Output vcf", shortName = "o", required = false)
- var outputVcf: File = _
-
- var minSampleDepth: Option[Int] = config("min_sample_depth")
- var minTotalDepth: Option[Int] = config("min_total_depth")
- var minAlternateDepth: Option[Int] = config("min_alternate_depth")
- var minSamplesPass: Option[Int] = config("min_samples_pass")
- var filterRefCalls: Boolean = config("filter_ref_calls", default = false)
-
- override def defaultCoreMemory = 3.0
-
- override def commandLine = super.commandLine +
- required("-I", inputVcf) +
- required("-o", outputVcf) +
- optional("--minSampleDepth", minSampleDepth) +
- optional("--minTotalDepth", minTotalDepth) +
- optional("--minAlternateDepth", minAlternateDepth) +
- optional("--minSamplesPass", minSamplesPass) +
- conditional(filterRefCalls, "--filterRefCalls")
-}
-
object VcfFilter extends ToolCommand {
/** Container class for a trio */
- protected case class Trio(child: String, father: String, mother: String) {
+ protected[tools] case class Trio(child: String, father: String, mother: String) {
def this(arg: String) = {
this(arg.split(":")(0), arg.split(":")(1), arg.split(":")(2))
}
@@ -208,9 +180,9 @@ object VcfFilter extends ToolCommand {
} else
invertedWriter.foreach(_.add(record))
counterTotal += 1
- if (counterTotal % 100000 == 0) logger.info(counterTotal + " variants processed, " + counterLeft + " left")
+ if (counterTotal % 100000 == 0) logger.info(s"$counterTotal variants processed, $counterLeft passed filter")
}
- logger.info(counterTotal + " variants processed, " + counterLeft + " left")
+ logger.info(s"$counterTotal variants processed, $counterLeft passed filter")
reader.close()
writer.close()
invertedWriter.foreach(_.close())
@@ -278,7 +250,7 @@ object VcfFilter extends ToolCommand {
}
/**
- * Checks if AD genotype field have a minimal value
+ * Checks if non-ref AD genotype field have a minimal value
* @param record VCF record
* @param minAlternateDepth minimal depth
* @param minSamplesPass Minimal number of samples to pass filter
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
similarity index 88%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index a051d2c33a4136aeeb813e6e956102644efa9520..960c4921debd6e58f45fa00bbb9dc0864dd11c60 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -21,11 +21,9 @@ import htsjdk.samtools.reference.FastaSequenceFile
import htsjdk.samtools.util.Interval
import htsjdk.variant.variantcontext.{ Allele, Genotype, VariantContext }
import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
-import nl.lumc.sasc.biopet.core.{ Reference, ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import scala.collection.mutable
@@ -38,89 +36,6 @@ import scala.util.Random
*
* Created by pjvan_thof on 1/10/15.
*/
-class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable with Reference {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input fastq", shortName = "I", required = true)
- var input: File = _
-
- @Input
- protected var index: File = null
-
- @Output
- protected var generalStats: File = null
-
- @Output
- protected var genotypeStats: File = null
-
- override def defaultCoreMemory = 3.0
- override def defaultThreads = 3
-
- protected var outputDir: File = _
-
- var infoTags: List[String] = Nil
- var genotypeTags: List[String] = Nil
- var allInfoTags = false
- var allGenotypeTags = false
- var reference: File = _
-
- override def beforeGraph(): Unit = {
- reference = referenceFasta()
- index = new File(input.getAbsolutePath + ".tbi")
- }
-
- /** Set output dir and a output file */
- def setOutputDir(dir: File): Unit = {
- outputDir = dir
- generalStats = new File(dir, "general.tsv")
- genotypeStats = new File(dir, "genotype-general.tsv")
- jobOutputFile = new File(dir, ".vcfstats.out")
- }
-
- /** Creates command to execute extension */
- override def commandLine = super.commandLine +
- required("-I", input) +
- required("-o", outputDir) +
- repeat("--infoTag", infoTags) +
- repeat("--genotypeTag", genotypeTags) +
- conditional(allInfoTags, "--allInfoTags") +
- conditional(allGenotypeTags, "--allGenotypeTags") +
- required("-R", reference)
-
- /** Returns general stats to the summary */
- def summaryStats: Map[String, Any] = {
- Map("info" -> (for (
- line <- Source.fromFile(generalStats).getLines().toList.tail;
- values = line.split("\t") if values.size >= 2 && !values(0).isEmpty
- ) yield values(0) -> values(1).toInt
- ).toMap)
- }
-
- /** return only general files to summary */
- def summaryFiles: Map[String, File] = Map(
- "general_stats" -> generalStats,
- "genotype_stats" -> genotypeStats
- )
-
- override def addToQscriptSummary(qscript: SummaryQScript, name: String): Unit = {
- val data = Source.fromFile(genotypeStats).getLines().map(_.split("\t")).toArray
-
- for (s <- 1 until data(0).size) {
- val sample = data(0)(s)
- val stats = Map("genotype" -> (for (f <- 1 until data.length) yield {
- data(f)(0) -> data(f)(s)
- }).toMap)
-
- val sum = new Summarizable {
- override def summaryFiles: Map[String, File] = Map()
- override def summaryStats: Map[String, Any] = stats
- }
-
- qscript.addSummarizable(sum, name, Some(sample))
- }
- }
-}
-
object VcfStats extends ToolCommand {
/** Commandline argument */
case class Args(inputFile: File = null,
@@ -136,44 +51,64 @@ object VcfStats extends ToolCommand {
generalWiggle: List[String] = Nil,
genotypeWiggle: List[String] = Nil) extends AbstractArgs
+ private val generalWiggleOptions = List("Total", "Biallelic", "ComplexIndel", "Filtered", "FullyDecoded", "Indel", "Mixed",
+ "MNP", "MonomorphicInSamples", "NotFiltered", "PointEvent", "PolymorphicInSamples",
+ "SimpleDeletion", "SimpleInsertion", "SNP", "StructuralIndel", "Symbolic",
+ "SymbolicOrSV", "Variant")
+
+ private val genotypeWiggleOptions = List("Total", "Het", "HetNonRef", "Hom", "HomRef", "HomVar", "Mixed", "NoCall", "NonInformative",
+ "Available", "Called", "Filtered", "Variant")
+
/** Parsing commandline arguments */
class OptParser extends AbstractOptParser {
- opt[File]('I', "inputFile") required () unbounded () valueName "<file>" action { (x, c) =>
+ opt[File]('I', "inputFile") required () unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
- }
- opt[File]('R', "referenceFile") required () unbounded () valueName "<file>" action { (x, c) =>
+ } validate {
+ x => if (x.exists) success else failure("Input VCF required")
+ } text "Input VCF file (required)"
+ opt[File]('R', "referenceFile") required () unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(referenceFile = x)
- }
- opt[File]('o', "outputDir") required () unbounded () valueName "<file>" action { (x, c) =>
+ } validate {
+ x => if (x.exists) success else failure("Reference file required")
+ } text "Fasta reference which was used to call input VCF (required)"
+ opt[File]('o', "outputDir") required () unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(outputDir = x)
- }
+ } validate {
+ x => if (x == null) failure("Output directory required") else success
+ } text "Path to directory for output (required)"
opt[File]('i', "intervals") unbounded () valueName ("<file>") action { (x, c) =>
c.copy(intervals = Some(x))
- }
+ } text "Path to interval (BED) file (optional)"
opt[String]("infoTag") unbounded () valueName "<tag>" action { (x, c) =>
c.copy(infoTags = x :: c.infoTags)
- }
+ } text "Summarize these info tags. Default is all tags"
opt[String]("genotypeTag") unbounded () valueName "<tag>" action { (x, c) =>
c.copy(genotypeTags = x :: c.genotypeTags)
- }
+ } text "Summarize these genotype tags. Default is all tags"
opt[Unit]("allInfoTags") unbounded () action { (x, c) =>
c.copy(allInfoTags = true)
- }
+ } text "Summarize all info tags. Default false"
opt[Unit]("allGenotypeTags") unbounded () action { (x, c) =>
c.copy(allGenotypeTags = true)
- }
+ } text "Summarize all genotype tags. Default false"
opt[Int]("binSize") unbounded () action { (x, c) =>
c.copy(binSize = x)
- }
+ } text "Binsize in estimated base pairs"
opt[Unit]("writeBinStats") unbounded () action { (x, c) =>
c.copy(writeBinStats = true)
- }
+ } text "Write bin statistics. Default False"
opt[String]("generalWiggle") unbounded () action { (x, c) =>
c.copy(generalWiggle = x :: c.generalWiggle, writeBinStats = true)
- }
+ } validate {
+ x => if (generalWiggleOptions.contains(x)) success else failure(s"""Nonexistent field $x""")
+ } text s"""Create a wiggle track with bin size <binSize> for any of the following statistics:
+ |${generalWiggleOptions.mkString(", ")}""".stripMargin
opt[String]("genotypeWiggle") unbounded () action { (x, c) =>
c.copy(genotypeWiggle = x :: c.genotypeWiggle, writeBinStats = true)
- }
+ } validate {
+ x => if (genotypeWiggleOptions.contains(x)) success else failure(s"""Non-existent field $x""")
+ } text s"""Create a wiggle track with bin size <binSize> for any of the following genotype fields:
+ |${genotypeWiggleOptions.mkString(", ")}""".stripMargin
}
/**
@@ -481,7 +416,7 @@ object VcfStats extends ToolCommand {
}
/** Function to check all general stats, all info expect sample/genotype specific stats */
- protected def checkGeneral(record: VariantContext, additionalTags: List[String]): Map[String, Map[String, Map[Any, Int]]] = {
+ protected[tools] def checkGeneral(record: VariantContext, additionalTags: List[String]): Map[String, Map[String, Map[Any, Int]]] = {
val buffer = mutable.Map[String, Map[Any, Int]]()
def addToBuffer(key: String, value: Any, found: Boolean): Unit = {
@@ -490,7 +425,7 @@ object VcfStats extends ToolCommand {
else buffer += key -> (map + (value -> map.getOrElse(value, 0)))
}
- buffer += "QUAL" -> Map(record.getPhredScaledQual -> 1)
+ buffer += "QUAL" -> Map(Math.round(record.getPhredScaledQual) -> 1)
addToBuffer("SampleDistribution-Het", record.getGenotypes.count(genotype => genotype.isHet), found = true)
addToBuffer("SampleDistribution-HetNonRef", record.getGenotypes.count(genotype => genotype.isHetNonRef), found = true)
@@ -537,7 +472,7 @@ object VcfStats extends ToolCommand {
}
/** Function to check sample/genotype specific stats */
- protected def checkGenotype(record: VariantContext, genotype: Genotype, additionalTags: List[String]): Map[String, Map[String, Map[Any, Int]]] = {
+ protected[tools] def checkGenotype(record: VariantContext, genotype: Genotype, additionalTags: List[String]): Map[String, Map[String, Map[Any, Int]]] = {
val buffer = mutable.Map[String, Map[Any, Int]]()
def addToBuffer(key: String, value: Any, found: Boolean): Unit = {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
index 995efcdd2925b8e739646e52a9e6a3e21a90813a..20a15dacacba466b41235f32e77062179ad5f0a4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
@@ -19,16 +19,13 @@ import java.io.{ File, PrintStream }
import java.text.DecimalFormat
import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.JavaConversions._
import scala.collection.mutable
import scala.collection.mutable.{ ListBuffer, Map }
-class VcfToTsv {
- // TODO: Queue wrapper
-}
-
+// TODO: Queue wrapper
object VcfToTsv extends ToolCommand {
case class Args(inputFile: File = null, outputFile: File = null, fields: List[String] = Nil, infoFields: List[String] = Nil,
sampleFields: List[String] = Nil, disableDefaults: Boolean = false,
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
similarity index 56%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
index 665bd2d34546f87483cf03b5846388a0c38f7969..2b764ec9c2c7d75b12dc0248eddca338957e2ee7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
@@ -16,52 +16,16 @@
package nl.lumc.sasc.biopet.tools
import java.io.File
+import java.util
-import htsjdk.variant.variantcontext.VariantContextBuilder
+import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf._
-import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, ToolCommand }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.VcfUtils.scalaListToJavaObjectArrayList
import scala.collection.JavaConversions._
-/**
- * Biopet extension for tool VcfWithVcf
- */
-class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input vcf file", shortName = "input", required = true)
- var input: File = _
-
- @Input(doc = "Secondary vcf file", shortName = "secondary", required = true)
- var secondaryVcf: File = _
-
- @Output(doc = "Output vcf file", shortName = "output", required = true)
- var output: File = _
-
- @Output(doc = "Output vcf file index", shortName = "output", required = true)
- private var outputIndex: File = _
-
- var fields: List[(String, String, Option[String])] = List()
-
- override def defaultCoreMemory = 2.0
-
- override def beforeGraph() {
- super.beforeGraph()
- if (output.getName.endsWith(".gz")) outputIndex = new File(output.getAbsolutePath + ".tbi")
- if (output.getName.endsWith(".vcf")) outputIndex = new File(output.getAbsolutePath + ".idx")
- if (fields.isEmpty) throw new IllegalArgumentException("No fields found for VcfWithVcf")
- }
-
- override def commandLine = super.commandLine +
- required("-I", input) +
- required("-o", output) +
- required("-s", secondaryVcf) +
- repeat("-f", fields.map(x => x._1 + ":" + x._2 + ":" + x._3.getOrElse("none")))
-}
-
/**
* This is a tool to annotate a vcf file with info value from a other vcf file
*
@@ -99,7 +63,7 @@ object VcfWithVcf extends ToolCommand {
| By default we will return all values found for a given field.
| With <method> the values will processed after getting it from the secondary VCF file, posible methods are:
| - max : takes maximum of found value, only works for numeric (integer/float) fields
- | - min : takes minemal of found value, only works for numeric (integer/float) fields
+ | - min : takes minimum of found value, only works for numeric (integer/float) fields
| - unique: takes only unique values """.stripMargin
opt[Boolean]("match") valueName "<Boolean>" maxOccurs 1 action { (x, c) =>
c.copy(matchAllele = x)
@@ -124,7 +88,7 @@ object VcfWithVcf extends ToolCommand {
for (x <- commandArgs.fields) {
if (header.hasInfoLine(x.outputField))
- throw new IllegalArgumentException("Field '" + x.outputField + "' already exist in input vcf")
+ throw new IllegalArgumentException("Field '" + x.outputField + "' already exists in input vcf")
if (!secondHeader.hasInfoLine(x.inputField))
throw new IllegalArgumentException("Field '" + x.inputField + "' does not exist in secondary vcf")
@@ -140,44 +104,11 @@ object VcfWithVcf extends ToolCommand {
var counter = 0
for (record <- reader) {
- val secondaryRecords = if (commandArgs.matchAllele) {
- secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList.
- filter(x => record.getAlternateAlleles.exists(x.hasAlternateAllele))
- } else {
- secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList
- }
+ val secondaryRecords = getSecondaryRecords(secondaryReader, record, commandArgs.matchAllele)
- val fieldMap = (for (
- f <- commandArgs.fields if secondaryRecords.exists(_.hasAttribute(f.inputField))
- ) yield {
- f.outputField -> (for (
- secondRecord <- secondaryRecords if secondRecord.hasAttribute(f.inputField)
- ) yield {
- secondRecord.getAttribute(f.inputField) match {
- case l: List[_] => l
- case x => List(x)
- }
- }).fold(Nil)(_ ::: _)
- }).toMap
-
- writer.add(fieldMap.foldLeft(new VariantContextBuilder(record))((builder, attribute) => {
- builder.attribute(attribute._1, commandArgs.fields.filter(_.outputField == attribute._1).head.fieldMethod match {
- case FieldMethod.max =>
- header.getInfoHeaderLine(attribute._1).getType match {
- case VCFHeaderLineType.Integer => Array(attribute._2.map(_.toString.toInt).max)
- case VCFHeaderLineType.Float => Array(attribute._2.map(_.toString.toFloat).max)
- case _ => throw new IllegalArgumentException("Type of field " + attribute._1 + " is not numeric")
- }
- case FieldMethod.min =>
- header.getInfoHeaderLine(attribute._1).getType match {
- case VCFHeaderLineType.Integer => Array(attribute._2.map(_.toString.toInt).min)
- case VCFHeaderLineType.Float => Array(attribute._2.map(_.toString.toFloat).min)
- case _ => throw new IllegalArgumentException("Type of field " + attribute._1 + " is not numeric")
- }
- case FieldMethod.unique => attribute._2.distinct.toArray
- case _ => attribute._2.toArray
- })
- }).make())
+ val fieldMap = createFieldMap(commandArgs.fields, secondaryRecords)
+
+ writer.add(createRecord(fieldMap, record, commandArgs.fields, header))
counter += 1
if (counter % 100000 == 0) {
@@ -192,4 +123,69 @@ object VcfWithVcf extends ToolCommand {
secondaryReader.close()
logger.info("Done")
}
+
+ /**
+ * Create Map of field -> List of attributes in secondary records
+ * @param fields List of Field
+ * @param secondaryRecords List of VariantContext with secondary records
+ * @return Map of fields and their values in secondary records
+ */
+ def createFieldMap(fields: List[Fields], secondaryRecords: List[VariantContext]): Map[String, List[Any]] = {
+ val fieldMap = (for (
+ f <- fields if secondaryRecords.exists(_.hasAttribute(f.inputField))
+ ) yield {
+ f.outputField -> (for (
+ secondRecord <- secondaryRecords if secondRecord.hasAttribute(f.inputField)
+ ) yield {
+ secondRecord.getAttribute(f.inputField) match {
+ case l: List[_] => l
+ case y: util.ArrayList[_] => y.toList
+ case x => List(x)
+ }
+ }).fold(Nil)(_ ::: _)
+ }).toMap
+ fieldMap
+ }
+
+ /**
+ * Get secondary records matching the query record
+ * @param secondaryReader reader for secondary records
+ * @param record query record
+ * @param matchAllele allele has to match query allele?
+ * @return List of VariantContext
+ */
+ def getSecondaryRecords(secondaryReader: VCFFileReader,
+ record: VariantContext, matchAllele: Boolean): List[VariantContext] = {
+ if (matchAllele) {
+ secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList.
+ filter(x => record.getAlternateAlleles.exists(x.hasAlternateAllele))
+ } else {
+ secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList
+ }
+ }
+
+ def createRecord(fieldMap: Map[String, List[Any]], record: VariantContext,
+ fields: List[Fields], header: VCFHeader): VariantContext = {
+ fieldMap.foldLeft(new VariantContextBuilder(record))((builder, attribute) => {
+ builder.attribute(attribute._1, fields.filter(_.outputField == attribute._1).head.fieldMethod match {
+ case FieldMethod.max =>
+ header.getInfoHeaderLine(attribute._1).getType match {
+ case VCFHeaderLineType.Integer => scalaListToJavaObjectArrayList(List(attribute._2.map(_.toString.toInt).max))
+ case VCFHeaderLineType.Float => scalaListToJavaObjectArrayList(List(attribute._2.map(_.toString.toFloat).max))
+ case _ => throw new IllegalArgumentException("Type of field " + attribute._1 + " is not numeric")
+ }
+ case FieldMethod.min =>
+ header.getInfoHeaderLine(attribute._1).getType match {
+ case VCFHeaderLineType.Integer => scalaListToJavaObjectArrayList(List(attribute._2.map(_.toString.toInt).min))
+ case VCFHeaderLineType.Float => scalaListToJavaObjectArrayList(List(attribute._2.map(_.toString.toFloat).min))
+ case _ => throw new IllegalArgumentException("Type of field " + attribute._1 + " is not numeric")
+ }
+ case FieldMethod.unique => scalaListToJavaObjectArrayList(attribute._2.distinct)
+ case _ => {
+ print(attribute._2.getClass.toString)
+ scalaListToJavaObjectArrayList(attribute._2)
+ }
+ })
+ }).make()
+ }
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
similarity index 91%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
index 1f5680c257cbbffe9e747e24109763a106063ec2..f9f0fe472686589f47c52b04d2c3e97a181a026e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
@@ -21,9 +21,7 @@ import htsjdk.tribble.TribbleException
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
import htsjdk.variant.vcf._
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.JavaConversions._
import scala.collection.mutable.{ Map => MMap }
@@ -37,28 +35,6 @@ import scala.collection.mutable.{ Map => MMap }
* 2) standard - parse as a standard VCF, where multiple transcripts occur in the same line
* Created by ahbbollen on 10/27/14.
*/
-
-class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
- javaMainClass = getClass.getName
-
- @Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
- var inputVCF: File = null
-
- @Output(doc = "Output VCF", shortName = "OutputFile", required = true)
- var outputVcf: File = null
-
- var mode: String = config("mode", default = "standard")
- var doNotRemove: Boolean = config("do_not_remove", default = false)
-
- override def defaultCoreMemory = 1.0
-
- override def commandLine = super.commandLine +
- required("-I", inputVCF) +
- required("-O", outputVcf) +
- required("-m", mode) +
- conditional(doNotRemove, "--do-not-remove")
-}
-
object VepNormalizer extends ToolCommand {
def main(args: Array[String]): Unit = {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
similarity index 93%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
index 845b4883f6c142a50187c70b50113ededdc84213..082ad2626b1667d4438857b64f6579cfc725f4af 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
@@ -17,44 +17,17 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
-import com.google.common.hash.{ BloomFilter, Funnel, PrimitiveSink }
+import com.google.common.hash.{ PrimitiveSink, Funnel, BloomFilter }
import htsjdk.samtools.{ QueryInterval, SAMFileWriter, SAMFileWriterFactory, SAMRecord, SamReader, SamReaderFactory, ValidationStringency }
import htsjdk.samtools.util.{ Interval, IntervalTreeMap }
-import htsjdk.tribble.AbstractFeatureReader.getFeatureReader
-import htsjdk.tribble.bed.BEDCodec
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.utils.ToolCommand
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import org.apache.commons.io.FilenameUtils.getExtension
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConverters._
import scala.io.Source
import scala.math.{ max, min }
-// TODO: finish implementation for usage in pipelines
-/**
- * WipeReads function class for usage in Biopet pipelines
- *
- * @param root Configuration object for the pipeline
- */
-class WipeReads(val root: Configurable) extends ToolCommandFuntion {
-
- javaMainClass = getClass.getName
-
- @Input(doc = "Input BAM file (must be indexed)", shortName = "I", required = true)
- var inputBam: File = null
-
- @Input(doc = "Interval file", shortName = "r", required = true)
- var intervalFile: File = null
-
- @Output(doc = "Output BAM", shortName = "o", required = true)
- var outputBam: File = null
-
- @Output(doc = "BAM containing discarded reads", shortName = "f", required = false)
- var discardedBam: File = null
-}
-
object WipeReads extends ToolCommand {
/** Creates a SamReader object from an input BAM file, ensuring it is indexed */
diff --git a/public/biopet-framework/src/test/resources/README.txt b/public/biopet-tools/src/test/resources/README.txt
similarity index 100%
rename from public/biopet-framework/src/test/resources/README.txt
rename to public/biopet-tools/src/test/resources/README.txt
diff --git a/public/biopet-framework/src/test/resources/VCFv3.vcf b/public/biopet-tools/src/test/resources/VCFv3.vcf
similarity index 100%
rename from public/biopet-framework/src/test/resources/VCFv3.vcf
rename to public/biopet-tools/src/test/resources/VCFv3.vcf
diff --git a/public/biopet-framework/src/test/resources/VEP_oneline.vcf b/public/biopet-tools/src/test/resources/VEP_oneline.vcf
similarity index 100%
rename from public/biopet-framework/src/test/resources/VEP_oneline.vcf
rename to public/biopet-tools/src/test/resources/VEP_oneline.vcf
diff --git a/public/biopet-framework/src/test/resources/VEP_oneline.vcf.gz b/public/biopet-tools/src/test/resources/VEP_oneline.vcf.gz
similarity index 100%
rename from public/biopet-framework/src/test/resources/VEP_oneline.vcf.gz
rename to public/biopet-tools/src/test/resources/VEP_oneline.vcf.gz
diff --git a/public/biopet-framework/src/test/resources/VEP_oneline.vcf.gz.tbi b/public/biopet-tools/src/test/resources/VEP_oneline.vcf.gz.tbi
similarity index 100%
rename from public/biopet-framework/src/test/resources/VEP_oneline.vcf.gz.tbi
rename to public/biopet-tools/src/test/resources/VEP_oneline.vcf.gz.tbi
diff --git a/public/biopet-framework/src/test/resources/chrQ.vcf b/public/biopet-tools/src/test/resources/chrQ.vcf
similarity index 100%
rename from public/biopet-framework/src/test/resources/chrQ.vcf
rename to public/biopet-tools/src/test/resources/chrQ.vcf
diff --git a/public/biopet-framework/src/test/resources/chrQ.vcf.gz b/public/biopet-tools/src/test/resources/chrQ.vcf.gz
similarity index 100%
rename from public/biopet-framework/src/test/resources/chrQ.vcf.gz
rename to public/biopet-tools/src/test/resources/chrQ.vcf.gz
diff --git a/public/biopet-framework/src/test/resources/chrQ.vcf.gz.tbi b/public/biopet-tools/src/test/resources/chrQ.vcf.gz.tbi
similarity index 100%
rename from public/biopet-framework/src/test/resources/chrQ.vcf.gz.tbi
rename to public/biopet-tools/src/test/resources/chrQ.vcf.gz.tbi
diff --git a/public/biopet-tools/src/test/resources/chrQ2.vcf b/public/biopet-tools/src/test/resources/chrQ2.vcf
new file mode 100644
index 0000000000000000000000000000000000000000..e49f468d7a6d54de23ed5e3d118d45a663c1cb63
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/chrQ2.vcf
@@ -0,0 +1,85 @@
+##fileformat=VCFv4.1
+##reference=file:///data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta
+##UnifiedGenotyperCommandLine=<ID=ApplyRecalibration,Version=3.1-1-g07a4bf8,Date="Sat Jun 14 16:58:07 CEST 2014",Epoch=1402757887567,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/Child_7006504.ug.chrom_merged.vcf)] recal_file=(RodBinding name=recal_file source=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.snp.recal) tranches_file=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.snp.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##UnifiedGenotyperCommandLine=<ID=ApplyRecalibration,Version=3.1-1-g07a4bf8,Date="Sat Jun 14 17:01:08 CEST 2014",Epoch=1402758068552,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.snp.recalibrated.vcf)] recal_file=(RodBinding name=recal_file source=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.indel.recal) tranches_file=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_ug/Child_7006504.indel.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##UnifiedGenotyperCommandLine=<ID=UnifiedGenotyper,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Child_7006504.ready.bam, /data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Mother_7006508.ready.bam, /data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Father_7006506.ready.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[chrM] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=BOTH pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=20.0 standard_min_confidence_threshold_for_emitting=20.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name=dbsnp source=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/dbsnp_137.hg19_nohap.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Sat Jun 14 15:20:24 CEST 2014",Epoch=1402752024377,Version=3.1-1-g07a4bf8>
+##HaplotypeCallerCommandLine=<ID=ApplyRecalibration,Version=3.1-1-g07a4bf8,Date="Sat Jun 14 22:28:02 CEST 2014",Epoch=1402777682364,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/Child_7006504.hc.chrom_merged.vcf)] recal_file=(RodBinding name=recal_file source=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.snp.recal) tranches_file=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.snp.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=SNP filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##HaplotypeCallerCommandLine=<ID=ApplyRecalibration,Version=3.1-1-g07a4bf8,Date="Sat Jun 14 22:31:13 CEST 2014",Epoch=1402777873043,CommandLineOptions="analysis_type=ApplyRecalibration input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false input=[(RodBinding name=input source=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.snp.recalibrated.vcf)] recal_file=(RodBinding name=recal_file source=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.indel.recal) tranches_file=/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/recalibration_hc/Child_7006504.indel.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 lodCutoff=null ignore_filter=null excludeFiltered=false mode=INDEL filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##HaplotypeCallerCommandLine=<ID=HaplotypeCaller,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Child_7006504.ready.bam, /data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Mother_7006508.ready.bam, /data/DIV5/KG/kg_wes_mr/runs/trio_7006504_run_00/trio_7006504/phase2/bams/Father_7006506.ready.bam] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[chrM] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/ucsc.hg19_nohap.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bam_compression=null disable_bam_indexing=null generate_md5=null simplifyBAM=null bamWriterType=CALLED_HAPLOTYPES dbsnp=(RodBinding name=dbsnp source=/data/DIV5/KG/references/gatk_bundle_2.5/hg19_nohap/dbsnp_137.hg19_nohap.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator] heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=20.0 standard_min_confidence_threshold_for_emitting=20.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false numPruningSamples=1 recoverDanglingHeads=false dontRecoverDanglingTails=false consensus=false emitRefConfidence=NONE GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false useFilteredReadsForAnnotations=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false pair_hmm_implementation=LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debug=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false",Date="Sat Jun 14 15:26:18 CEST 2014",Epoch=1402752378803,Version=3.1-1-g07a4bf8>
+##INFO=<ID=DN,Number=1,Type=Integer,Description="inDbSNP">
+##INFO=<ID=DT,Number=0,Type=Flag,Description="in1000Genomes">
+##INFO=<ID=DA,Number=1,Type=String,Description="allelesDBSNP">
+##INFO=<ID=FG,Number=.,Type=String,Description="functionGVS">
+##INFO=<ID=FD,Number=.,Type=String,Description="functionDBSNP">
+##INFO=<ID=GM,Number=.,Type=String,Description="accession">
+##INFO=<ID=GL,Number=.,Type=String,Description="geneList">
+##INFO=<ID=AAC,Number=.,Type=String,Description="aminoAcids">
+##INFO=<ID=PP,Number=.,Type=String,Description="proteinPosition">
+##INFO=<ID=CDP,Number=.,Type=String,Description="cDNAPosition">
+##INFO=<ID=PH,Number=.,Type=String,Description="polyPhen">
+##INFO=<ID=CP,Number=1,Type=String,Description="scorePhastCons">
+##INFO=<ID=CG,Number=1,Type=String,Description="consScoreGERP">
+##INFO=<ID=AA,Number=1,Type=String,Description="chimpAllele">
+##INFO=<ID=CN,Number=.,Type=String,Description="CNV">
+##INFO=<ID=HA,Number=1,Type=String,Description="AfricanHapMapFreq">
+##INFO=<ID=HE,Number=1,Type=String,Description="EuropeanHapMapFreq">
+##INFO=<ID=HC,Number=1,Type=String,Description="AsianHapMapFreq">
+##INFO=<ID=DG,Number=0,Type=Flag,Description="hasGenotypes">
+##INFO=<ID=DV,Number=.,Type=String,Description="dbSNPValidation">
+##INFO=<ID=RM,Number=.,Type=String,Description="repeatMasker">
+##INFO=<ID=RT,Number=.,Type=String,Description="tandemRepeat">
+##INFO=<ID=CA,Number=0,Type=Flag,Description="clinicalAssociation">
+##INFO=<ID=DSP,Number=1,Type=Integer,Description="distanceToSplice">
+##INFO=<ID=GS,Number=.,Type=String,Description="granthamScore">
+##INFO=<ID=MR,Number=.,Type=String,Description="microRNAs">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
+##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
+##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
+##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
+##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=GATKCaller,Number=.,Type=String,Description="GATK variant caller used to call the variant">
+##INFO=<ID=PartOfCompound,Number=.,Type=String,Description="Whether the record was originally part of a record containing compound variants">
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -1.4714 <= x < -0.3324">
+##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -6.093">
+##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -6.093 <= x < -1.4714">
+##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -4.8126 <= x < 0.2264">
+##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -39474.9285">
+##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -39474.9285 <= x < -4.8126">
+##FILTER=<ID=TooHigh1000GAF,Description="Allele frequency in 1000G is more than 5%">
+##FILTER=<ID=TooHighGoNLAF,Description="Allele frequency in 1000G is more than 5%">
+##FILTER=<ID=IndexNotCalled,Description="Position in index sample is not called">
+##FILTER=<ID=IndexIsVariant,Description="Index call is a variant">
+##FILTER=<ID=InArtificialChrom,Description="Variant found in an artificial chromosome">
+##FILTER=<ID=IsIntergenic,Description="Variant found in intergenic region">
+##contig=<ID=chrQ,length=16571>
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|AA_MAF|EA_MAF|ALLELE_NUM|DISTANCE|STRAND|CLIN_SIG|SYMBOL|SYMBOL_SOURCE|GMAF|HGVSc|HGVSp|AFR_MAF|AMR_MAF|ASN_MAF|EUR_MAF|PUBMED">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Child_7006504 Father_7006506 Mother_7006508
+chrQ 50 rs199537431 T A 1541.12 PASS FG=intron;FD=unknown;GM=NM_152486.2;GL=SAMD11;CP=0.000;CG=-1.630;CN=2294,3274,30362,112930;DSP=107;AC=2;AF=0.333;AN=6;BaseQRankSum=4.068;DB;DP=124;FS=1.322;MLEAC=2;MLEAF=0.333;MQ=60.0;MQ0=0;MQRankSum=-0.197;QD=19.03;RPA=1,2;RU=A;ReadPosRankSum=-0.424;STR;VQSLOD=0.079;culprit=FS;GATKCaller=UG,HC;CSQ=A|ENSESTG00000013623|ENSESTT00000034081|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||||A:0.0078|ENSESTT00000034081.1:c.306-110_306-109insA||||||,A|CCDS2.2|CCDS2.2|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||||A:0.0078|CCDS2.2:c.306-110_306-109insA||||||,A|ENSESTG00000013623|ENSESTT00000034116|Transcript|upstream_gene_variant||||||rs199537431|||1|3610|1||||A:0.0078|||||||,A|ENSESTG00000013623|ENSESTT00000034091|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||||A:0.0078|ENSESTT00000034091.1:c.306-110_306-109insA||||||,A|ENSESTG00000013623|ENSESTT00000034102|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||||A:0.0078|ENSESTT00000034102.1:c.29-110_29-109insA||||||,A|148398|XM_005244723.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244723.1:c.306-110_306-109insA||||||,A|148398|XM_005244724.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244724.1:c.306-110_306-109insA||||||,A|148398|XM_005244725.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244725.1:c.306-110_306-109insA||||||,A|148398|NM_152486.2|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|NM_152486.2:c.306-110_306-109insA||||||,A|148398|XM_005244727.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244727.1:c.306-110_306-109insA||||||,A|148398|XM_005244726.1|Transcript|intron_variant&feature_elongation||||||rs199537431|||1||1||SAMD11||A:0.0078|XM_005244726.1:c.306-110_306-109insA|||||| GT:AD:DP:GQ:PL 0/1:24,21:45:99:838,0,889 0/1:17,19:36:99:744,0,603 0/0:42,0:43:99:0,126,1717
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+
+ #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14
+#1 100.0000% 100.0000% 0.0000% 100.0000% 0.0000% 0.0000% 0.0000% 100.0000% 100.0000% 100.0000% 0.0000% 0.0000% 0.0000% 0.0000%
+#2 100.0000% 100.0000% 0.0000% 100.0000% 0.0000% 0.0000% 0.0000% 100.0000% 100.0000% 100.0000% 0.0000% 0.0000% 0.0000% 0.0000%
+#3 NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN%
+#4 100.0000% 100.0000% 0.0000% 100.0000% 0.0000% 0.0000% 0.0000% 100.0000% 100.0000% 100.0000% 0.0000% 0.0000% 0.0000% 0.0000%
+#5 NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN%
+#6 NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN%
+#7 NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN%
+#8 100.0000% 100.0000% 0.0000% 100.0000% 0.0000% 0.0000% 0.0000% 100.0000% 100.0000% 100.0000% 0.0000% 0.0000% 0.0000% 0.0000%
+#9 100.0000% 100.0000% 0.0000% 100.0000% 0.0000% 0.0000% 0.0000% 100.0000% 100.0000% 100.0000% 0.0000% 0.0000% 0.0000% 0.0000%
+#10 100.0000% 100.0000% 0.0000% 100.0000% 0.0000% 0.0000% 0.0000% 100.0000% 100.0000% 100.0000% 0.0000% 0.0000% 0.0000% 0.0000%
+#11 NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN%
+#12 NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN%
+#13 NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN%
+#14 NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN% NaN%
+
diff --git a/public/biopet-tools/src/test/resources/flagstat_summary.txt b/public/biopet-tools/src/test/resources/flagstat_summary.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7984915cab425c8bd94dd0a22eae60e0407f518
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/flagstat_summary.txt
@@ -0,0 +1,16 @@
+{
+ "Duplicates" : 0,
+ "NotPrimaryAlignment" : 0,
+ "All" : 1,
+ "ReadNegativeStrand" : 0,
+ "ProperPair" : 1,
+ "MateUnmapped" : 0,
+ "ReadFailsVendorQualityCheck" : 0,
+ "Mapped" : 1,
+ "SupplementaryAlignment" : 0,
+ "MateNegativeStrand" : 1,
+ "FirstOfPair" : 1,
+ "ReadPaired" : 1,
+ "SecondaryOrSupplementary" : 0,
+ "SecondOfPair" : 0
+}
\ No newline at end of file
diff --git a/public/biopet-tools/src/test/resources/log4j.properties b/public/biopet-tools/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/biopet-tools/src/test/resources/mini.transcriptome.fa b/public/biopet-tools/src/test/resources/mini.transcriptome.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d86c34faa29af176b6dd1a5d098c16d4e618039f
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/mini.transcriptome.fa
@@ -0,0 +1,17 @@
+>ENST00000529862 havana:known chromosome:GRCh38:11:105194440:105194946:-1 gene:ENSG00000254767 gene_biotype:unprocessed_pseudogene transcript_biotype:unprocessed_pseudogene
+ATGAATAATAATGGGAAATATCAACATAAGTCTTGAAAATTACTTTATTCTACTGGGTCT
+TTCTAATTGACCTCCTCTGGAAATAGTTATTTTTGTAGTTCTCTTGATATTCTGCTTCAT
+GACACTGATAGGCAAGCTGTTCAGCATCATTCTGTCATACCTGGACTCCCATCCCCACAC
+TCTCGGTACTTATTCTCTTTTCTGGATTTCTGCTACACCATCAGTTCCATCTTTTAATTA
+CAGTACAATCTCTGGGGCCCACAGAAGAACATCTCTTATGCCAGTGGTATGATTCAAATT
+TATTTTGTTCTCACACTGGGAACCATGGATTGCGCTCTACTGGTGGTGATGTCCAGGACT
+GTGATGCAGCTGGACACAGACACTTGCCTTATACTGTTGTTATGGCTGTGGCTTTTTGGG
+TAAGTAGCTTTACCAACTCAGCATTTGATTCCTTTTTTACCTTCTGGGTAACCCTGTGTG
+GACATCACTATTATGCTTACATCTTTA
+>ENST00000528941 havana:known chromosome:GRCh38:11:105246880:105247060:-1 gene:ENSG00000255336 gene_biotype:unprocessed_pseudogene transcript_biotype:unprocessed_pseudogene
+TATTCATAATTAAAGTCATACTTCAGCAAGCTGGCTTTAAATATACAACATATAATTCTT
+TTAAATCAGACTCTCTGAATCCATGACCGCCATGTCTTCATGAAGCTGTCCTTCCTCAAT
+CCCCATCTGTTTTAAGGGTTCCACCCATGTTCTTCCTTAGCACCCTGAGTATTTACTCTA
+T
+>ENST99999999999 havana:known chromosome:GRCh38:11:105246880:105247060:-1 gene:ENSG99999999999 gene_biotype:unprocessed_pseudogene transcript_biotype:unprocessed_pseudogene
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
diff --git a/public/biopet-tools/src/test/resources/no_sample.tsv b/public/biopet-tools/src/test/resources/no_sample.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..81ccc2453208183e7fa8a8a2b0748f2a4d8f6716
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/no_sample.tsv
@@ -0,0 +1,3 @@
+library bam
+Lib_ID_1 MyFirst.bam
+Lib_ID_2 MySecond.bam
diff --git a/public/biopet-tools/src/test/resources/number.tsv b/public/biopet-tools/src/test/resources/number.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..0a76d53e6db7be2f331f440f72f48003d63ef49f
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/number.tsv
@@ -0,0 +1,3 @@
+sample library bam
+1 5 MyFirst.bam
+2 6 MySecond.bam
diff --git a/public/biopet-framework/src/test/resources/paired01.bam b/public/biopet-tools/src/test/resources/paired01.bam
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired01.bam
rename to public/biopet-tools/src/test/resources/paired01.bam
diff --git a/public/biopet-framework/src/test/resources/paired01.bam.bai b/public/biopet-tools/src/test/resources/paired01.bam.bai
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired01.bam.bai
rename to public/biopet-tools/src/test/resources/paired01.bam.bai
diff --git a/public/biopet-tools/src/test/resources/paired01.pileup b/public/biopet-tools/src/test/resources/paired01.pileup
new file mode 100644
index 0000000000000000000000000000000000000000..559c87b964c35b428bd913b32fd769873e24fd14
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/paired01.pileup
@@ -0,0 +1,320 @@
+chrQ 50 N 1 ^]T E
+chrQ 51 N 1 A E
+chrQ 52 N 1 C F
+chrQ 53 N 1 G F
+chrQ 54 N 1 T G
+chrQ 55 N 1 A G
+chrQ 56 N 1 C H
+chrQ 57 N 1 G H
+chrQ 58 N 1 T I
+chrQ 59 N 1 A$ I
+chrQ 90 N 1 ^]a E
+chrQ 91 N 1 t E
+chrQ 92 N 1 g F
+chrQ 93 N 1 c F
+chrQ 94 N 1 a G
+chrQ 95 N 1 t G
+chrQ 96 N 1 g H
+chrQ 97 N 1 c H
+chrQ 98 N 1 a I
+chrQ 99 N 1 t$ I
+chrQ 150 N 1 ^]A G
+chrQ 151 N 1 A G
+chrQ 152 N 1 A G
+chrQ 153 N 1 A G
+chrQ 154 N 1 A G
+chrQ 155 N 1 G G
+chrQ 156 N 1 G G
+chrQ 157 N 1 G G
+chrQ 158 N 1 G G
+chrQ 159 N 1 G$ G
+chrQ 190 N 1 ^]g G
+chrQ 191 N 1 g G
+chrQ 192 N 1 g G
+chrQ 193 N 1 g G
+chrQ 194 N 1 g G
+chrQ 195 N 1 a G
+chrQ 196 N 1 a G
+chrQ 197 N 1 a G
+chrQ 198 N 1 a G
+chrQ 199 N 1 a$ G
+chrQ 250 N 1 ^]A G
+chrQ 251 N 1 A G
+chrQ 252 N 1 A G
+chrQ 253 N 1 A G
+chrQ 254 N 1 A G
+chrQ 255 N 1 G G
+chrQ 256 N 1 G G
+chrQ 257 N 1 G G
+chrQ 258 N 1 G G
+chrQ 259 N 1 G$ G
+chrQ 290 N 1 ^]g G
+chrQ 291 N 1 g G
+chrQ 292 N 1 g G
+chrQ 293 N 1 g G
+chrQ 294 N 1 g G
+chrQ 295 N 1 a G
+chrQ 296 N 1 a G
+chrQ 297 N 1 a G
+chrQ 298 N 1 a G
+chrQ 299 N 1 a$ G
+chrQ 450 N 1 ^]C E
+chrQ 451 N 1 G E
+chrQ 452 N 1 T F
+chrQ 453 N 1 A F
+chrQ 454 N 1 C G
+chrQ 455 N 1 G G
+chrQ 456 N 1 T H
+chrQ 457 N 1 A H
+chrQ 458 N 1 C I
+chrQ 459 N 1 G$ I
+chrQ 490 N 1 ^]g E
+chrQ 491 N 1 c E
+chrQ 492 N 1 a F
+chrQ 493 N 1 t F
+chrQ 494 N 1 g G
+chrQ 495 N 1 c G
+chrQ 496 N 1 a H
+chrQ 497 N 1 t H
+chrQ 498 N 1 g I
+chrQ 499 N 1 c$ I
+chrQ 650 N 1 ^]T H
+chrQ 651 N 1 T H
+chrQ 652 N 1 T H
+chrQ 653 N 1 T H
+chrQ 654 N 1 T H
+chrQ 655 N 1 C H
+chrQ 656 N 1 C H
+chrQ 657 N 1 C H
+chrQ 658 N 1 C H
+chrQ 659 N 1 C$ H
+chrQ 690 N 1 ^]c H
+chrQ 691 N 1 c H
+chrQ 692 N 1 c H
+chrQ 693 N 1 c H
+chrQ 694 N 1 c H
+chrQ 695 N 1 t H
+chrQ 696 N 1 t H
+chrQ 697 N 1 t H
+chrQ 698 N 1 t H
+chrQ 699 N 1 t$ H
+chrQ 890 N 1 ^]T E
+chrQ 891 N 1 A E
+chrQ 892 N 1 C F
+chrQ 893 N 1 G F
+chrQ 894 N 1 T G
+chrQ 895 N 1 > G
+chrQ 896 N 1 > G
+chrQ 897 N 1 > G
+chrQ 898 N 1 > G
+chrQ 899 N 1 > G
+chrQ 900 N 1 > G
+chrQ 901 N 1 > G
+chrQ 902 N 1 > G
+chrQ 903 N 1 > G
+chrQ 904 N 1 > G
+chrQ 905 N 1 > G
+chrQ 906 N 1 > G
+chrQ 907 N 1 > G
+chrQ 908 N 1 > G
+chrQ 909 N 1 > G
+chrQ 910 N 1 > G
+chrQ 911 N 1 > G
+chrQ 912 N 1 > G
+chrQ 913 N 1 > G
+chrQ 914 N 1 > G
+chrQ 915 N 1 > G
+chrQ 916 N 1 > G
+chrQ 917 N 1 > G
+chrQ 918 N 1 > G
+chrQ 919 N 1 > G
+chrQ 920 N 1 > G
+chrQ 921 N 1 > G
+chrQ 922 N 1 > G
+chrQ 923 N 1 > G
+chrQ 924 N 1 > G
+chrQ 925 N 1 > G
+chrQ 926 N 1 > G
+chrQ 927 N 1 > G
+chrQ 928 N 1 > G
+chrQ 929 N 1 > G
+chrQ 930 N 1 > G
+chrQ 931 N 1 > G
+chrQ 932 N 1 > G
+chrQ 933 N 1 > G
+chrQ 934 N 1 > G
+chrQ 935 N 1 > G
+chrQ 936 N 1 > G
+chrQ 937 N 1 > G
+chrQ 938 N 1 > G
+chrQ 939 N 1 > G
+chrQ 940 N 1 > G
+chrQ 941 N 1 > G
+chrQ 942 N 1 > G
+chrQ 943 N 1 > G
+chrQ 944 N 1 > G
+chrQ 945 N 1 > G
+chrQ 946 N 1 > G
+chrQ 947 N 1 > G
+chrQ 948 N 1 > G
+chrQ 949 N 1 > G
+chrQ 950 N 1 > G
+chrQ 951 N 1 > G
+chrQ 952 N 1 > G
+chrQ 953 N 1 > G
+chrQ 954 N 1 > G
+chrQ 955 N 1 > G
+chrQ 956 N 1 > G
+chrQ 957 N 1 > G
+chrQ 958 N 1 > G
+chrQ 959 N 1 > G
+chrQ 960 N 1 > G
+chrQ 961 N 1 > G
+chrQ 962 N 1 > G
+chrQ 963 N 1 > G
+chrQ 964 N 1 > G
+chrQ 965 N 1 > G
+chrQ 966 N 1 > G
+chrQ 967 N 1 > G
+chrQ 968 N 1 > G
+chrQ 969 N 1 > G
+chrQ 970 N 1 > G
+chrQ 971 N 1 > G
+chrQ 972 N 1 > G
+chrQ 973 N 1 > G
+chrQ 974 N 1 > G
+chrQ 975 N 1 > G
+chrQ 976 N 1 > G
+chrQ 977 N 1 > G
+chrQ 978 N 1 > G
+chrQ 979 N 1 > G
+chrQ 980 N 1 > G
+chrQ 981 N 1 > G
+chrQ 982 N 1 > G
+chrQ 983 N 1 > G
+chrQ 984 N 1 > G
+chrQ 985 N 1 > G
+chrQ 986 N 1 > G
+chrQ 987 N 1 > G
+chrQ 988 N 1 > G
+chrQ 989 N 1 > G
+chrQ 990 N 1 > G
+chrQ 991 N 1 > G
+chrQ 992 N 1 > G
+chrQ 993 N 1 > G
+chrQ 994 N 1 > G
+chrQ 995 N 1 > G
+chrQ 996 N 1 > G
+chrQ 997 N 1 > G
+chrQ 998 N 1 > G
+chrQ 999 N 1 > G
+chrQ 1000 N 1 > G
+chrQ 1001 N 1 > G
+chrQ 1002 N 1 > G
+chrQ 1003 N 1 > G
+chrQ 1004 N 1 > G
+chrQ 1005 N 1 > G
+chrQ 1006 N 1 > G
+chrQ 1007 N 1 > G
+chrQ 1008 N 1 > G
+chrQ 1009 N 1 > G
+chrQ 1010 N 1 > G
+chrQ 1011 N 1 > G
+chrQ 1012 N 1 > G
+chrQ 1013 N 1 > G
+chrQ 1014 N 1 > G
+chrQ 1015 N 1 > G
+chrQ 1016 N 1 > G
+chrQ 1017 N 1 > G
+chrQ 1018 N 1 > G
+chrQ 1019 N 1 > G
+chrQ 1020 N 1 > G
+chrQ 1021 N 1 > G
+chrQ 1022 N 1 > G
+chrQ 1023 N 1 > G
+chrQ 1024 N 1 > G
+chrQ 1025 N 1 > G
+chrQ 1026 N 1 > G
+chrQ 1027 N 1 > G
+chrQ 1028 N 1 > G
+chrQ 1029 N 1 > G
+chrQ 1030 N 1 > G
+chrQ 1031 N 1 > G
+chrQ 1032 N 1 > G
+chrQ 1033 N 1 > G
+chrQ 1034 N 1 > G
+chrQ 1035 N 1 > G
+chrQ 1036 N 1 > G
+chrQ 1037 N 1 > G
+chrQ 1038 N 1 > G
+chrQ 1039 N 1 > G
+chrQ 1040 N 1 > G
+chrQ 1041 N 1 > G
+chrQ 1042 N 1 > G
+chrQ 1043 N 1 > G
+chrQ 1044 N 1 > G
+chrQ 1045 N 1 > G
+chrQ 1046 N 1 > G
+chrQ 1047 N 1 > G
+chrQ 1048 N 1 > G
+chrQ 1049 N 1 > G
+chrQ 1050 N 1 > G
+chrQ 1051 N 1 > G
+chrQ 1052 N 1 > G
+chrQ 1053 N 1 > G
+chrQ 1054 N 1 > G
+chrQ 1055 N 1 > G
+chrQ 1056 N 1 > G
+chrQ 1057 N 1 > G
+chrQ 1058 N 1 > G
+chrQ 1059 N 1 > G
+chrQ 1060 N 1 > G
+chrQ 1061 N 1 > G
+chrQ 1062 N 1 > G
+chrQ 1063 N 1 > G
+chrQ 1064 N 1 > G
+chrQ 1065 N 1 > G
+chrQ 1066 N 1 > G
+chrQ 1067 N 1 > G
+chrQ 1068 N 1 > G
+chrQ 1069 N 1 > G
+chrQ 1070 N 1 > G
+chrQ 1071 N 1 > G
+chrQ 1072 N 1 > G
+chrQ 1073 N 1 > G
+chrQ 1074 N 1 > G
+chrQ 1075 N 1 > G
+chrQ 1076 N 1 > G
+chrQ 1077 N 1 > G
+chrQ 1078 N 1 > G
+chrQ 1079 N 1 > G
+chrQ 1080 N 1 > G
+chrQ 1081 N 1 > G
+chrQ 1082 N 1 > G
+chrQ 1083 N 1 > G
+chrQ 1084 N 1 > G
+chrQ 1085 N 1 > G
+chrQ 1086 N 1 > G
+chrQ 1087 N 1 > G
+chrQ 1088 N 1 > G
+chrQ 1089 N 1 > G
+chrQ 1090 N 1 > G
+chrQ 1091 N 1 > G
+chrQ 1092 N 1 > G
+chrQ 1093 N 1 > G
+chrQ 1094 N 1 > G
+chrQ 1095 N 1 A G
+chrQ 1096 N 1 C H
+chrQ 1097 N 1 G H
+chrQ 1098 N 1 T I
+chrQ 1099 N 1 A$ I
+chrQ 1140 N 1 ^]a E
+chrQ 1141 N 1 t E
+chrQ 1142 N 1 g F
+chrQ 1143 N 1 c F
+chrQ 1144 N 1 a G
+chrQ 1145 N 1 t G
+chrQ 1146 N 1 g H
+chrQ 1147 N 1 c H
+chrQ 1148 N 1 a I
+chrQ 1149 N 1 t$ I
diff --git a/public/biopet-framework/src/test/resources/paired01.sam b/public/biopet-tools/src/test/resources/paired01.sam
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired01.sam
rename to public/biopet-tools/src/test/resources/paired01.sam
diff --git a/public/biopet-framework/src/test/resources/paired01a.fq b/public/biopet-tools/src/test/resources/paired01a.fq
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired01a.fq
rename to public/biopet-tools/src/test/resources/paired01a.fq
diff --git a/public/biopet-framework/src/test/resources/paired01b.fq b/public/biopet-tools/src/test/resources/paired01b.fq
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired01b.fq
rename to public/biopet-tools/src/test/resources/paired01b.fq
diff --git a/public/biopet-framework/src/test/resources/paired02.bam b/public/biopet-tools/src/test/resources/paired02.bam
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired02.bam
rename to public/biopet-tools/src/test/resources/paired02.bam
diff --git a/public/biopet-framework/src/test/resources/paired02.bam.bai b/public/biopet-tools/src/test/resources/paired02.bam.bai
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired02.bam.bai
rename to public/biopet-tools/src/test/resources/paired02.bam.bai
diff --git a/public/biopet-framework/src/test/resources/paired02.sam b/public/biopet-tools/src/test/resources/paired02.sam
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired02.sam
rename to public/biopet-tools/src/test/resources/paired02.sam
diff --git a/public/biopet-framework/src/test/resources/paired03.bam b/public/biopet-tools/src/test/resources/paired03.bam
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired03.bam
rename to public/biopet-tools/src/test/resources/paired03.bam
diff --git a/public/biopet-framework/src/test/resources/paired03.bam.bai b/public/biopet-tools/src/test/resources/paired03.bam.bai
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired03.bam.bai
rename to public/biopet-tools/src/test/resources/paired03.bam.bai
diff --git a/public/biopet-framework/src/test/resources/paired03.sam b/public/biopet-tools/src/test/resources/paired03.sam
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired03.sam
rename to public/biopet-tools/src/test/resources/paired03.sam
diff --git a/public/biopet-framework/src/test/resources/rrna01.bed b/public/biopet-tools/src/test/resources/rrna01.bed
similarity index 100%
rename from public/biopet-framework/src/test/resources/rrna01.bed
rename to public/biopet-tools/src/test/resources/rrna01.bed
diff --git a/public/biopet-framework/src/test/resources/rrna01.gtf b/public/biopet-tools/src/test/resources/rrna01.gtf
similarity index 100%
rename from public/biopet-framework/src/test/resources/rrna01.gtf
rename to public/biopet-tools/src/test/resources/rrna01.gtf
diff --git a/public/biopet-framework/src/test/resources/rrna01.refFlat b/public/biopet-tools/src/test/resources/rrna01.refFlat
similarity index 100%
rename from public/biopet-framework/src/test/resources/rrna01.refFlat
rename to public/biopet-tools/src/test/resources/rrna01.refFlat
diff --git a/public/biopet-framework/src/test/resources/rrna02.bed b/public/biopet-tools/src/test/resources/rrna02.bed
similarity index 100%
rename from public/biopet-framework/src/test/resources/rrna02.bed
rename to public/biopet-tools/src/test/resources/rrna02.bed
diff --git a/public/biopet-tools/src/test/resources/sageAllGenesTest.tsv b/public/biopet-tools/src/test/resources/sageAllGenesTest.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..602518753b0b9a24a18c6561fbb0b6aabd99a2fe
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/sageAllGenesTest.tsv
@@ -0,0 +1,3 @@
+ENSG00000255336
+ENSG00000254767
+ENSG99999999999
diff --git a/public/biopet-tools/src/test/resources/sageNoAntiTest.tsv b/public/biopet-tools/src/test/resources/sageNoAntiTest.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..84f1b39db543978adcf0f29ae27c96aacfe823f7
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/sageNoAntiTest.tsv
@@ -0,0 +1 @@
+ENSG99999999999
diff --git a/public/biopet-tools/src/test/resources/sageNoTagsTest.tsv b/public/biopet-tools/src/test/resources/sageNoTagsTest.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..84f1b39db543978adcf0f29ae27c96aacfe823f7
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/sageNoTagsTest.tsv
@@ -0,0 +1 @@
+ENSG99999999999
diff --git a/public/biopet-tools/src/test/resources/sageTest.tsv b/public/biopet-tools/src/test/resources/sageTest.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..080395ff9049459f7a43dfc131beb05367d89b7c
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/sageTest.tsv
@@ -0,0 +1,9 @@
+#tag firstTag AllTags FirstAntiTag AllAntiTags
+CATGAAGACATGGCGGTCATG ENSG00000255336
+CATGAAGCAGAATATCAAGAG ENSG00000254767
+CATGACACTGATAGGCAAGCT ENSG00000254767
+CATGACCGCCATGTCTTCATG ENSG00000255336
+CATGGATTGCGCTCTACTGGT ENSG00000254767 ENSG00000254767
+CATGGGTGGAACCCTTAAAAC ENSG00000255336 ENSG00000255336
+CATGGTTCCCAGTGTGAGAAC ENSG00000254767 ENSG00000254767
+CATGTTCTTCCTTAGCACCCT ENSG00000255336 ENSG00000255336
diff --git a/public/biopet-tools/src/test/resources/same.tsv b/public/biopet-tools/src/test/resources/same.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..e82fcbb3b50a1c8a613480ad0b0ef76673a0060c
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/same.tsv
@@ -0,0 +1,3 @@
+sample library bam
+Sample_ID_1 Lib_ID_1 MyFirst.bam
+Sample_ID_1 Lib_ID_1 MySecond.bam
diff --git a/public/biopet-tools/src/test/resources/sample.tsv b/public/biopet-tools/src/test/resources/sample.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..3c67fc7c1cbc58ad00d7869ed1275b9a85e96cf3
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/sample.tsv
@@ -0,0 +1,3 @@
+sample library bam
+Sample_ID_1 Lib_ID_1 MyFirst.bam
+Sample_ID_2 Lib_ID_2 MySecond.bam
diff --git a/public/biopet-framework/src/test/resources/single01.bam b/public/biopet-tools/src/test/resources/single01.bam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single01.bam
rename to public/biopet-tools/src/test/resources/single01.bam
diff --git a/public/biopet-framework/src/test/resources/single01.bam.bai b/public/biopet-tools/src/test/resources/single01.bam.bai
similarity index 100%
rename from public/biopet-framework/src/test/resources/single01.bam.bai
rename to public/biopet-tools/src/test/resources/single01.bam.bai
diff --git a/public/biopet-framework/src/test/resources/single01.fq b/public/biopet-tools/src/test/resources/single01.fq
similarity index 100%
rename from public/biopet-framework/src/test/resources/single01.fq
rename to public/biopet-tools/src/test/resources/single01.fq
diff --git a/public/biopet-framework/src/test/resources/single01.sam b/public/biopet-tools/src/test/resources/single01.sam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single01.sam
rename to public/biopet-tools/src/test/resources/single01.sam
diff --git a/public/biopet-framework/src/test/resources/single02.bam b/public/biopet-tools/src/test/resources/single02.bam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single02.bam
rename to public/biopet-tools/src/test/resources/single02.bam
diff --git a/public/biopet-framework/src/test/resources/single02.bam.bai b/public/biopet-tools/src/test/resources/single02.bam.bai
similarity index 100%
rename from public/biopet-framework/src/test/resources/single02.bam.bai
rename to public/biopet-tools/src/test/resources/single02.bam.bai
diff --git a/public/biopet-framework/src/test/resources/single02.sam b/public/biopet-tools/src/test/resources/single02.sam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single02.sam
rename to public/biopet-tools/src/test/resources/single02.sam
diff --git a/public/biopet-framework/src/test/resources/single03.bam b/public/biopet-tools/src/test/resources/single03.bam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single03.bam
rename to public/biopet-tools/src/test/resources/single03.bam
diff --git a/public/biopet-framework/src/test/resources/single03.bam.bai b/public/biopet-tools/src/test/resources/single03.bam.bai
similarity index 100%
rename from public/biopet-framework/src/test/resources/single03.bam.bai
rename to public/biopet-tools/src/test/resources/single03.bam.bai
diff --git a/public/biopet-framework/src/test/resources/single03.sam b/public/biopet-tools/src/test/resources/single03.sam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single03.sam
rename to public/biopet-tools/src/test/resources/single03.sam
diff --git a/public/biopet-framework/src/test/resources/single04.bam b/public/biopet-tools/src/test/resources/single04.bam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single04.bam
rename to public/biopet-tools/src/test/resources/single04.bam
diff --git a/public/biopet-framework/src/test/resources/single04.bam.bai b/public/biopet-tools/src/test/resources/single04.bam.bai
similarity index 100%
rename from public/biopet-framework/src/test/resources/single04.bam.bai
rename to public/biopet-tools/src/test/resources/single04.bam.bai
diff --git a/public/biopet-framework/src/test/resources/single04.sam b/public/biopet-tools/src/test/resources/single04.sam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single04.sam
rename to public/biopet-tools/src/test/resources/single04.sam
diff --git a/public/biopet-framework/src/test/resources/single05.bam b/public/biopet-tools/src/test/resources/single05.bam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single05.bam
rename to public/biopet-tools/src/test/resources/single05.bam
diff --git a/public/biopet-framework/src/test/resources/single05.bam.bai b/public/biopet-tools/src/test/resources/single05.bam.bai
similarity index 100%
rename from public/biopet-framework/src/test/resources/single05.bam.bai
rename to public/biopet-tools/src/test/resources/single05.bam.bai
diff --git a/public/biopet-framework/src/test/resources/single05.sam b/public/biopet-tools/src/test/resources/single05.sam
similarity index 100%
rename from public/biopet-framework/src/test/resources/single05.sam
rename to public/biopet-tools/src/test/resources/single05.sam
diff --git a/public/biopet-tools/src/test/resources/tagCount.tsv b/public/biopet-tools/src/test/resources/tagCount.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..64181d09a20cdab0c5bfc4792dc081fe5fd0f222
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/tagCount.tsv
@@ -0,0 +1,8 @@
+CATGAAGACATGGCGGTCATG 20
+CATGAAGCAGAATATCAAGAG 25
+CATGACACTGATAGGCAAGCT 30
+CATGACCGCCATGTCTTCATG 35
+CATGGATTGCGCTCTACTGGT 40
+CATGGGTGGAACCCTTAAAAC 45
+CATGGTTCCCAGTGTGAGAAC 50
+CATGTTCTTCCTTAGCACCCT 55
diff --git a/public/biopet-tools/src/test/resources/test.summary.json b/public/biopet-tools/src/test/resources/test.summary.json
new file mode 100644
index 0000000000000000000000000000000000000000..aff9e962e4662f9f76f4a53f2a8fe0557ecb92d4
--- /dev/null
+++ b/public/biopet-tools/src/test/resources/test.summary.json
@@ -0,0 +1,17 @@
+{
+ "samples" : {
+ "016" : {
+ "libraries" : {
+ "L001" : {
+ "flexiprep" : {
+ "settings" : {
+ "skip_trim" : false,
+ "skip_clip" : false,
+ "paired" : true
+ }
+ }
+ }
+ }
+ }
+ }
+}
diff --git a/public/biopet-tools/src/test/resources/unvep_online.vcf.gz b/public/biopet-tools/src/test/resources/unvep_online.vcf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..f102295f99d0bc62e25de296b84dc6610930a683
Binary files /dev/null and b/public/biopet-tools/src/test/resources/unvep_online.vcf.gz differ
diff --git a/public/biopet-tools/src/test/resources/unvep_online.vcf.gz.tbi b/public/biopet-tools/src/test/resources/unvep_online.vcf.gz.tbi
new file mode 100644
index 0000000000000000000000000000000000000000..bb43ff545f591dd276973e7158919e6d14c78f23
Binary files /dev/null and b/public/biopet-tools/src/test/resources/unvep_online.vcf.gz.tbi differ
diff --git a/public/biopet-framework/src/test/resources/unvepped.vcf b/public/biopet-tools/src/test/resources/unvepped.vcf
similarity index 100%
rename from public/biopet-framework/src/test/resources/unvepped.vcf
rename to public/biopet-tools/src/test/resources/unvepped.vcf
diff --git a/public/biopet-framework/src/test/resources/unvepped.vcf.gz b/public/biopet-tools/src/test/resources/unvepped.vcf.gz
similarity index 100%
rename from public/biopet-framework/src/test/resources/unvepped.vcf.gz
rename to public/biopet-tools/src/test/resources/unvepped.vcf.gz
diff --git a/public/biopet-framework/src/test/resources/unvepped.vcf.gz.tbi b/public/biopet-tools/src/test/resources/unvepped.vcf.gz.tbi
similarity index 100%
rename from public/biopet-framework/src/test/resources/unvepped.vcf.gz.tbi
rename to public/biopet-tools/src/test/resources/unvepped.vcf.gz.tbi
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..ebe393bfab7bdb8fedec024319e99a5b0ec29a07
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
@@ -0,0 +1,73 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.variant.vcf.VCFFileReader
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+import org.scalatest.mock.MockitoSugar
+import org.mockito.Mockito._
+
+/**
+ * Created by ahbbollen on 13-8-15.
+ */
+class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import BastyGenerateFasta._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val vepped_path = resourcePath("/VEP_oneline.vcf")
+ val vepped = new File(vepped_path)
+ val bam_path = resourcePath("/paired01.bam")
+ val chrQ_path = resourcePath("/chrQ.vcf.gz")
+ val chrQRef_path = resourcePath("/fake_chrQ.fa")
+ val bam = new File(resourcePath("/paired01.bam"))
+ val chrQ = new File(resourcePath("/chrQ.vcf.gz"))
+ val chrQRef = new File(resourcePath("/fake_chrQ.fa"))
+
+ @Test def testMainVcf = {
+ val tmp = File.createTempFile("basty_out", ".fa")
+ val tmppath = tmp.getAbsolutePath
+ tmp.deleteOnExit()
+
+ val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
+ main(arguments)
+ }
+
+ @Test def testMainVcfAndBam = {
+ val tmp = File.createTempFile("basty_out", ".fa")
+ val tmppath = tmp.getAbsolutePath
+ tmp.deleteOnExit()
+
+ val arguments = Array("-V", chrQ_path, "--outputVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
+ main(arguments)
+ }
+
+ @Test def testMainVcfAndBamMore = {
+ val tmp = File.createTempFile("basty_out", ".fa")
+ val tmppath = tmp.getAbsolutePath
+ tmp.deleteOnExit()
+
+ val arguments = Array("-V", chrQ_path, "--outputConsensus", tmppath, "--outputConsensusVariants", tmppath, "--bamFile", bam_path, "--sampleName", "Child_7006504", "--reference", chrQRef_path, "--outputName", "test")
+ main(arguments)
+ }
+
+ @Test def testGetMaxAllele = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ val child = mock[Args]
+ when(child.sampleName) thenReturn "Child_7006504"
+ val father = mock[Args]
+ when(father.sampleName) thenReturn "Father_7006506"
+
+ getMaxAllele(record)(child) shouldBe "C-"
+ getMaxAllele(record)(father) shouldBe "CA"
+
+ }
+
+}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..758cb6be6d6aa0a75c2ec1830e0fa3334beb7626
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
@@ -0,0 +1,62 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.samtools.SamReaderFactory
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * Created by ahbbollen on 26-8-15.
+ */
+class BiopetFlagstatTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import BiopetFlagstat._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val bam = new File(resourcePath("/paired01.bam"))
+ val report = new File(resourcePath("/flagstat_report.txt"))
+ val summary = new File(resourcePath("/flagstat_summary.txt"))
+ val crossReport = new File(resourcePath("/flagstat_crossreport.txt"))
+ val crossTrue = new File(resourcePath("/flagstat_crosstrue.txt"))
+
+ val record = SamReaderFactory.makeDefault().open(bam).iterator().next()
+ val processor = new FlagstatCollector
+ processor.loadDefaultFunctions()
+ processor.loadRecord(record)
+
+ @Test
+ def testReport() = {
+ processor.report shouldBe Source.fromFile(report).mkString
+ }
+
+ @Test
+ def testSummary() = {
+ processor.summary shouldBe Source.fromFile(summary).mkString
+ }
+
+ @Test
+ def testCrossReport() = {
+ processor.crossReport() shouldBe Source.fromFile(crossReport).mkString
+ }
+
+ @Test
+ def testCrossReportTrue() = {
+ processor.crossReport(true) shouldBe Source.fromFile(crossTrue).mkString
+ }
+
+ @Test
+ def testMain() = {
+ //TODO: Test output file
+ val output = File.createTempFile("testMain", ".biopetflagstat")
+ main(Array("-I", bam.getAbsolutePath, "-o", output.toString))
+ }
+
+}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
similarity index 74%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
index 6a99b92d3fd3b9ba16f9c09e67094cff1e40bedf..476e8e6230caa6bd1051a683459ca28566516699 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
@@ -15,8 +15,11 @@
*/
package nl.lumc.sasc.biopet.tools
+import java.io.File
import java.nio.file.Paths
+import htsjdk.samtools.{ SamReaderFactory, SamReader }
+import htsjdk.variant.vcf.VCFFileReader
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
@@ -38,6 +41,7 @@ class CheckAllelesVcfInBamTest extends TestNGSuite with MockitoSugar with Matche
val vcf = resourcePath("/chrQ.vcf")
val bam = resourcePath("/single01.bam")
+ val vcf2 = new File(resourcePath("/chrQ2.vcf.gz"))
val rand = new Random()
@Test def testOutputTypeVcf() = {
@@ -58,4 +62,19 @@ class CheckAllelesVcfInBamTest extends TestNGSuite with MockitoSugar with Matche
main(arguments)
}
+ @Test
+ def testCheckAllelesNone() = {
+ val variant = new File(vcf)
+ val samRecord = SamReaderFactory.makeDefault().open(new File(bam)).iterator().next()
+ val varRecord = new VCFFileReader(variant, false).iterator().next()
+ checkAlleles(samRecord, varRecord) shouldBe None
+ }
+
+ @Test
+ def testCheckAlleles() = {
+ val samRecord = SamReaderFactory.makeDefault().open(new File(bam)).iterator().next()
+ val varRecord = new VCFFileReader(vcf2).iterator().next()
+ checkAlleles(samRecord, varRecord) shouldBe Some("T")
+ }
+
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..ffa8be0bcb6c2cf15bf0ad00efeeb54e903eb3df
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
@@ -0,0 +1,39 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by ahbbollen on 27-8-15.
+ */
+class FastqSplitterTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import FastqSplitter._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val fq = resourcePath("/paired01a.fq")
+
+ @Test
+ def testMain() = {
+ val temp = File.createTempFile("out", ".fastq")
+
+ val args = Array("-I", fq, "-o", temp.getAbsolutePath)
+ main(args)
+ }
+
+ @Test
+ def testManyOutMain() = {
+ val files = (0 until 10).map(_ => File.createTempFile("out", ".fastq"))
+ var args = Array("-I", fq)
+ files.foreach(x => args ++= Array("-o", x.getAbsolutePath))
+ main(args)
+ }
+
+}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..b6de2f8bcca896e8979c2e21fc5bb8651524610a
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
@@ -0,0 +1,64 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.samtools.{ SamReaderFactory, QueryInterval }
+import nl.lumc.sasc.biopet.tools.FastqSplitter._
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.immutable.Nil
+
+/**
+ * Created by ahbbollen on 27-8-15.
+ */
+class FindRepeatsPacBioTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import FindRepeatsPacBio._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val bed = resourcePath("/rrna01.bed")
+ val bam = resourcePath("/paired01.bam")
+
+ @Test
+ def testMain() = {
+
+ val outputFile = File.createTempFile("repeats", ".tsv")
+ val args = Array("-I", bam, "-b", bed, "-o", outputFile.toString)
+ main(args)
+ }
+
+ @Test
+ def testResult() = {
+ val samReader = SamReaderFactory.makeDefault().open(new File(bam))
+ val header = samReader.getFileHeader
+ val record = samReader.iterator().next()
+ val interval = new QueryInterval(header.getSequenceIndex("chrQ"), 50, 55)
+ val result = procesSamrecord(record, interval)
+
+ result.isEmpty shouldBe false
+
+ result.get.samRecord shouldEqual record
+ result.get.beginDel should be >= 0
+ result.get.endDel should be >= 0
+ }
+
+ @Test
+ def testResultObject = {
+ val record = SamReaderFactory.makeDefault().open(new File(bam)).iterator().next()
+ val result = new Result
+ result.samRecord = record
+
+ result.samRecord shouldEqual record
+ result.beginDel shouldBe 0
+ result.endDel shouldBe 0
+ result.dels shouldEqual Nil
+ result.ins shouldEqual Nil
+ }
+
+}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MergeTablesTest.scala
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..032f9a913373c0f3be617e45cc26a928ca69821d
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
@@ -0,0 +1,78 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.samtools.reference.IndexedFastaSequenceFile
+import htsjdk.variant.variantcontext.Allele
+import htsjdk.variant.vcf.VCFFileReader
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.JavaConversions._
+
+/**
+ * Created by ahbbollen on 27-8-15.
+ */
+class MpileupToVcfTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import MpileupToVcf._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val pileup = resourcePath("/paired01.pileup")
+
+ @Test
+ def testMain() = {
+ val tmp = File.createTempFile("mpileup", ".vcf")
+ val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath)
+
+ main(args)
+ }
+
+ @Test
+ def validateOutVcf() = {
+ val tmp = File.createTempFile("mpileup", ".vcf")
+ val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath, "--minDP", "1", "--minAP", "1")
+ main(args)
+
+ val vcfReader = new VCFFileReader(tmp, false)
+
+ // VariantContexts validate on creation
+ // therefore we just have to loop through them
+
+ vcfReader.foreach(_ => 1)
+
+ }
+
+ @Test
+ def extraValidateOutVcf() = {
+ val tmp = File.createTempFile("mpileup", ".vcf")
+ val args = Array("-I", pileup, "--sample", "test", "-o", tmp.getAbsolutePath, "--minDP", "1", "--minAP", "1")
+ main(args)
+
+ val vcfReader = new VCFFileReader(tmp, false)
+
+ val fasta = resourcePath("/chrQ_allN.fa")
+
+ val sequenceFile = new IndexedFastaSequenceFile(new File(fasta))
+ val sequenceDict = sequenceFile.getSequenceDictionary
+
+ for (record <- vcfReader) {
+ val alleles = record.getAlleles.toSet
+ var ref_alleles = alleles -- record.getAlternateAlleles.toSet
+
+ ref_alleles.size should be >= 1
+
+ val realRef = Allele.create(sequenceFile.getSubsequenceAt(record.getContig,
+ record.getStart, record.getEnd).getBases, true)
+
+ for (ref <- ref_alleles) {
+ record.extraStrictValidation(ref, realRef, Set(""))
+ }
+ }
+ }
+}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..41db9e3ae268a62860fd3fbe9a27e4430165429e
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
@@ -0,0 +1,47 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.samtools.fastq.FastqReader
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.JavaConversions._
+
+/**
+ * Created by ahbbollen on 28-8-15.
+ */
+class PrefixFastqTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import PrefixFastq._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val fq = resourcePath("/paired01a.fq")
+
+ @Test
+ def testMain() = {
+ val temp = File.createTempFile("out", ".fastq")
+
+ val args = Array("-i", fq, "-o", temp.getAbsolutePath, "-s", "AAA")
+ main(args)
+ }
+
+ @Test
+ def testOutput() = {
+ val temp = File.createTempFile("out", ".fastq")
+
+ val args = Array("-i", fq, "-o", temp.getAbsolutePath, "-s", "AAA")
+ main(args)
+
+ val reader = new FastqReader(temp)
+
+ for (read <- reader.iterator()) {
+ read.getReadString.startsWith("AAA") shouldBe true
+ }
+ }
+}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..15d3074c95313c6f2a084c41b4d0a4787bdedddb
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
@@ -0,0 +1,30 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by ahbbollen on 28-8-15.
+ */
+class SageCountFastqTest extends TestNGSuite with MockitoSugar with Matchers {
+ import SageCountFastq._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val fq = resourcePath("/paired01a.fq")
+
+ @Test
+ def testMain() = {
+ val temp = File.createTempFile("out", ".fastq")
+
+ val args = Array("-I", fq, "-o", temp.getAbsolutePath)
+ main(args)
+ }
+
+}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..48038ea6f476fd89a945f53cf3d3608661fbcc9c
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
@@ -0,0 +1,112 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.biojava3.core.sequence.DNASequence
+import org.biojava3.core.sequence.io.FastaReaderHelper
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.JavaConversions._
+
+import scala.io.Source
+
+/**
+ * Created by ahbbollen on 7-9-15.
+ */
+class SageCreateLibaryTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import SageCreateLibrary._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ @Test
+ def testMain = {
+
+ val input = resourcePath("/mini.transcriptome.fa")
+ val output = File.createTempFile("sageCreateLibrary", ".tsv")
+ val noTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ val antiTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ val allGenesOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+
+ val args = Array("-I", input, "-o", output.getAbsolutePath, "--tag", "CATG",
+ "--length", "17", "--noTagsOutput", noTagsOutput.getAbsolutePath, "--noAntiTagsOutput",
+ antiTagsOutput.getAbsolutePath, "--allGenesOutput", allGenesOutput.getAbsolutePath)
+
+ noException should be thrownBy main(args)
+
+ val args2 = Array("-I", input, "-o", output.getAbsolutePath, "--tag", "CATG",
+ "--length", "17")
+ noException should be thrownBy main(args2)
+ val args3 = Array("-I", input, "-o", output.getAbsolutePath, "--tag", "CATG",
+ "--length", "17", "--noTagsOutput", noTagsOutput.getAbsolutePath)
+ noException should be thrownBy main(args3)
+
+ }
+
+ @Test
+ def testOutPut = {
+ val input = resourcePath("/mini.transcriptome.fa")
+ val output = File.createTempFile("sageCreateLibrary", ".tsv")
+ val noTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ val antiTagsOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+ val allGenesOutput = File.createTempFile("sageCreateLibrary", ".tsv")
+
+ val args = Array("-I", input, "-o", output.getAbsolutePath, "--tag", "CATG",
+ "--length", "17", "--noTagsOutput", noTagsOutput.getAbsolutePath, "--noAntiTagsOutput",
+ antiTagsOutput.getAbsolutePath, "--allGenesOutput", allGenesOutput.getAbsolutePath)
+ main(args)
+
+ Source.fromFile(output).mkString should equal(
+ Source.fromFile(new File(resourcePath("/sageTest.tsv"))).mkString
+ )
+
+ Source.fromFile(noTagsOutput).mkString should equal(
+ Source.fromFile(new File(resourcePath("/sageNoTagsTest.tsv"))).mkString
+ )
+
+ Source.fromFile(antiTagsOutput).mkString should equal(
+ Source.fromFile(new File(resourcePath("/sageNoAntiTest.tsv"))).mkString
+ )
+
+ Source.fromFile(allGenesOutput).mkString should equal(
+ Source.fromFile(new File(resourcePath("/sageAllGenesTest.tsv"))).mkString
+ )
+ }
+
+ @Test
+ def testGetTags = {
+ val input = resourcePath("/mini.transcriptome.fa")
+
+ val reader = FastaReaderHelper.readFastaDNASequence(new File(input))
+
+ val records = reader.iterator.toList
+ val tagRegex = ("CATG" + "[CATG]{" + 17 + "}").r
+
+ val record1 = records(0)
+ val record2 = records(1)
+ val record3 = records(2)
+
+ val result1 = getTags(record1._1, record1._2, tagRegex)
+ val result2 = getTags(record2._1, record2._2, tagRegex)
+ val result3 = getTags(record3._1, record3._2, tagRegex)
+
+ result1.allTags.size shouldBe 2
+ result1.allAntiTags.size shouldBe 2
+ result1.firstTag shouldBe "CATGGATTGCGCTCTACTGGT"
+ result1.firstAntiTag shouldBe "CATGGTTCCCAGTGTGAGAAC"
+
+ result2.allTags.size shouldBe 2
+ result2.allAntiTags.size shouldBe 2
+ result2.firstTag shouldBe "CATGTTCTTCCTTAGCACCCT"
+ result2.firstAntiTag shouldBe "CATGGGTGGAACCCTTAAAAC"
+
+ result3.allTags.size shouldBe 0
+ result3.allAntiTags.size shouldBe 0
+ }
+
+}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..b47c507856ec251878057a3823d47d57160045e9
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
@@ -0,0 +1,67 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * Created by ahbbollen on 7-9-15.
+ */
+class SageCreateTagCountsTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import SageCreateTagCounts._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ @Test
+ def testMain = {
+ val input = resourcePath("/tagCount.tsv")
+ val tagLib = resourcePath("/sageTest.tsv")
+
+ val sense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ val allSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ val antiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ val allAntiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+
+ noException should be thrownBy main(Array("-I", input, "--tagLib", tagLib,
+ "--countSense", sense.getAbsolutePath, "--countAllSense", allSense.getAbsolutePath,
+ "--countAntiSense", antiSense.getAbsolutePath, "--countAllAntiSense", allAntiSense.getAbsolutePath))
+ noException should be thrownBy main(Array("-I", input, "--tagLib", tagLib,
+ "--countSense", sense.getAbsolutePath, "--countAllSense", allSense.getAbsolutePath,
+ "--countAntiSense", antiSense.getAbsolutePath))
+ noException should be thrownBy main(Array("-I", input, "--tagLib", tagLib,
+ "--countSense", sense.getAbsolutePath, "--countAllSense", allSense.getAbsolutePath))
+ noException should be thrownBy main(Array("-I", input, "--tagLib", tagLib,
+ "--countSense", sense.getAbsolutePath))
+ noException should be thrownBy main(Array("-I", input, "--tagLib", tagLib))
+
+ }
+
+ @Test
+ def testOutput = {
+ val input = resourcePath("/tagCount.tsv")
+ val tagLib = resourcePath("/sageTest.tsv")
+
+ val sense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ val allSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ val antiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+ val allAntiSense = File.createTempFile("SageCreateTagCountsTEst", ".tsv")
+
+ main(Array("-I", input, "--tagLib", tagLib, "--countSense", sense.getAbsolutePath,
+ "--countAllSense", allSense.getAbsolutePath, "--countAntiSense", antiSense.getAbsolutePath,
+ "--countAllAntiSense", allAntiSense.getAbsolutePath))
+
+ Source.fromFile(sense).mkString should equal("ENSG00000254767\t40\nENSG00000255336\t55\n")
+ Source.fromFile(allSense).mkString should equal("ENSG00000254767\t70\nENSG00000255336\t90\n")
+ Source.fromFile(antiSense).mkString should equal("ENSG00000254767\t50\nENSG00000255336\t45\n")
+ Source.fromFile(allAntiSense).mkString should equal("ENSG00000254767\t75\nENSG00000255336\t65\n")
+ }
+
+}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..9866ad47a8efbfad5f34868b82fe415f6e6b8c28
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
@@ -0,0 +1,79 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by ahbbollen on 28-8-15.
+ */
+class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
+ import SamplesTsvToJson._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ @Test
+ def testCorrectSampleTsv = {
+ val tsv = resourcePath("/sample.tsv")
+ val output = File.createTempFile("testCorrectSampleTsv", ".json")
+
+ noException should be thrownBy main(Array("-i", tsv, "-o", output.toString))
+ }
+
+ @Test
+ def testNoSampleColumn() = {
+ val tsv = resourcePath("/no_sample.tsv")
+ val output = File.createTempFile("testNoSampleColumn", ".json")
+ val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv, "-o", output.toString))
+ thrown.getMessage should equal("Sample column does not exist in: " + tsv)
+ }
+
+ @Test
+ def testNumberInLibs = {
+ val tsv = resourcePath("/number.tsv")
+ val output = File.createTempFile("testNumberInLibs", ".json")
+ val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv, "-o", output.toString))
+ thrown.getMessage should equal("Sample or library may not start with a number")
+ }
+
+ @Test
+ def testSampleIDs = {
+ val tsv = resourcePath("/same.tsv")
+ val output = File.createTempFile("testSampleIDs", ".json")
+ val thrown = the[IllegalStateException] thrownBy main(Array("-i", tsv, "-o", output.toString))
+ thrown.getMessage should equal("Combination of Sample_ID_1 and Lib_ID_1 is found multiple times")
+
+ }
+
+ @Test
+ def testJson = {
+ val tsv = new File(resourcePath("/sample.tsv"))
+ val json = stringFromInputs(List(tsv))
+
+ json should equal(
+ """|{
+ | "samples" : {
+ | "Sample_ID_1" : {
+ | "libraries" : {
+ | "Lib_ID_1" : {
+ | "bam" : "MyFirst.bam"
+ | }
+ | }
+ | },
+ | "Sample_ID_2" : {
+ | "libraries" : {
+ | "Lib_ID_2" : {
+ | "bam" : "MySecond.bam"
+ | }
+ | }
+ | }
+ | }
+ |}""".stripMargin)
+ }
+
+}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
similarity index 97%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
index d9180aec45025b68e9830227110ca9320571b683..c9dd5e290c3cd4da97c58198da2a596258ed0c64 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
@@ -101,4 +101,6 @@ class SeqStatTest extends TestNGSuite with MockitoSugar with Matchers {
val parsed = parseArgs(args)
parsed.fastq shouldBe resourceFile("/paired01a.fq")
}
+
+ // TODO: Shared state here. Calling main changes the state, which causes other tests to fail
}
\ No newline at end of file
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..6071fceaaed85a943a4f973ac713d24e8b708952
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
@@ -0,0 +1,73 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import nl.lumc.sasc.biopet.tools.SamplesTsvToJson._
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import nl.lumc.sasc.biopet.utils.summary.Summary
+
+/**
+ * Created by ahbbollen on 31-8-15.
+ */
+class SummaryToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
+ import SummaryToTsv._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ @Test
+ def testMain = {
+ val tsv = resourcePath("/test.summary.json")
+ val output = File.createTempFile("main", "tsv")
+
+ noException should be thrownBy main(Array("-s", tsv, "-p", "something=flexiprep:settings:skip_trim",
+ "-m", "root", "-o", output.toString))
+ noException should be thrownBy main(Array("-s", tsv, "-p", "something=flexiprep:settings:skip_trim",
+ "-m", "sample", "-o", output.toString))
+ noException should be thrownBy main(Array("-s", tsv, "-p", "something=flexiprep:settings:skip_trim",
+ "-m", "lib", "-o", output.toString))
+ }
+
+ @Test
+ def testHeader = {
+ val tsv = resourcePath("/test.summary.json")
+ val path = List("something=flexiprep:settings:skip_trim")
+
+ val paths = path.map(x => {
+ val split = x.split("=", 2)
+ split(0) -> split(1).split(":")
+ }).toMap
+
+ createHeader(paths) should equal("\tsomething")
+ }
+
+ @Test
+ def testLine = {
+ val tsv = resourcePath("/test.summary.json")
+ val path = List("something=flexiprep:settings:skip_trim")
+
+ val paths = path.map(x => {
+ val split = x.split("=", 2)
+ split(0) -> split(1).split(":")
+ }).toMap
+
+ val summary = new Summary(new File(tsv))
+ val values = fetchValues(summary, paths)
+
+ val line = values.head._2.keys.map(x => createLine(paths, values, x)).head
+ line should equal("value\t")
+ val sample_values = fetchValues(summary, paths, true, false)
+ val sample_line = sample_values.head._2.keys.map(x => createLine(paths, sample_values, x)).head
+ sample_line should equal("016\t")
+
+ val lib_values = fetchValues(summary, paths, false, true)
+ val lib_line = lib_values.head._2.keys.map(x => createLine(paths, lib_values, x)).head
+ lib_line should equal("016-L001\tfalse")
+ }
+
+}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..80fe1980eccad9932e0472ae28242ae93e6b6420
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
@@ -0,0 +1,209 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.variant.variantcontext.GenotypeType
+import htsjdk.variant.vcf.VCFFileReader
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.util.Random
+
+/**
+ * Test class for [[VcfFilter]]
+ *
+ * Created by ahbbollen on 9-4-15.
+ */
+class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import VcfFilter._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val vepped_path = resourcePath("/VEP_oneline.vcf")
+ val vepped = new File(vepped_path)
+ val rand = new Random()
+
+ @Test def testOutputTypeVcf() = {
+ val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf"
+ val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
+ main(arguments)
+ }
+
+ @Test def testOutputTypeBcf() = {
+ val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".bcf"
+ val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
+ main(arguments)
+ }
+
+ @Test def testOutputTypeVcfGz() = {
+ val tmp_path = "/tmp/VcfFilter_" + rand.nextString(10) + ".vcf.gz"
+ val arguments: Array[String] = Array("-I", vepped_path, "-o", tmp_path)
+ main(arguments)
+ }
+
+ @Test def testHasGenotype() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ hasGenotype(record, List(("Child_7006504", GenotypeType.HET))) shouldBe true
+ hasGenotype(record, List(("Child_7006504", GenotypeType.HOM_VAR))) shouldBe false
+ hasGenotype(record, List(("Child_7006504", GenotypeType.HOM_REF))) shouldBe false
+ hasGenotype(record, List(("Child_7006504", GenotypeType.NO_CALL))) shouldBe false
+ hasGenotype(record, List(("Child_7006504", GenotypeType.MIXED))) shouldBe false
+
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HET))) shouldBe false
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_VAR))) shouldBe false
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_REF))) shouldBe true
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.NO_CALL))) shouldBe false
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.MIXED))) shouldBe false
+
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HOM_REF), ("Child_7006504", GenotypeType.HET))) shouldBe true
+ hasGenotype(record, List(("Mother_7006508", GenotypeType.HET), ("Child_7006504", GenotypeType.HOM_REF))) shouldBe false
+ }
+
+ @Test def testMinQualScore() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ minQualscore(record, 2000) shouldBe false
+ minQualscore(record, 1000) shouldBe true
+
+ }
+
+ @Test def testHasNonRefCalls() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ hasNonRefCalls(record) shouldBe true
+ }
+
+ @Test def testHasCalls() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ hasCalls(record) shouldBe true
+ }
+
+ @Test def testHasMinDP() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ hasMinTotalDepth(record, 100) shouldBe true
+ hasMinTotalDepth(record, 200) shouldBe false
+ }
+
+ @Test def testHasMinSampleDP() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ hasMinSampleDepth(record, 30, 1) shouldBe true
+ hasMinSampleDepth(record, 30, 2) shouldBe true
+ hasMinSampleDepth(record, 30, 3) shouldBe true
+ hasMinSampleDepth(record, 40, 1) shouldBe true
+ hasMinSampleDepth(record, 40, 2) shouldBe true
+ hasMinSampleDepth(record, 40, 3) shouldBe false
+ hasMinSampleDepth(record, 50, 1) shouldBe false
+ hasMinSampleDepth(record, 50, 2) shouldBe false
+ hasMinSampleDepth(record, 50, 3) shouldBe false
+ }
+
+ @Test def testHasMinSampleAD() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ minAlternateDepth(record, 0, 3) shouldBe true
+ minAlternateDepth(record, 10, 2) shouldBe true
+ minAlternateDepth(record, 10, 3) shouldBe false
+ minAlternateDepth(record, 20, 1) shouldBe true
+ minAlternateDepth(record, 20, 2) shouldBe false
+ }
+
+ @Test def testMustHaveVariant() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ mustHaveVariant(record, List("Child_7006504")) shouldBe true
+ mustHaveVariant(record, List("Child_7006504", "Father_7006506")) shouldBe true
+ mustHaveVariant(record, List("Child_7006504", "Father_7006506", "Mother_7006508")) shouldBe false
+ }
+
+ @Test def testSameGenotype() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ notSameGenotype(record, "Child_7006504", "Father_7006506") shouldBe false
+ notSameGenotype(record, "Child_7006504", "Mother_7006508") shouldBe true
+ notSameGenotype(record, "Father_7006506", "Mother_7006508") shouldBe true
+ }
+
+ @Test def testfilterHetVarToHomVar() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ filterHetVarToHomVar(record, "Child_7006504", "Father_7006506") shouldBe true
+ filterHetVarToHomVar(record, "Child_7006504", "Mother_7006508") shouldBe true
+ filterHetVarToHomVar(record, "Father_7006506", "Mother_7006508") shouldBe true
+ }
+
+ @Test def testDeNovo() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ denovoInSample(record, "Child_7006504") shouldBe false
+ denovoInSample(record, "Father_7006506") shouldBe false
+ denovoInSample(record, "Mother_7006508") shouldBe false
+ }
+
+ @Test def testResToDom() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+ val trio = new Trio("Child_7006504", "Father_7006506", "Mother_7006508")
+
+ resToDom(record, List(trio)) shouldBe false
+ }
+
+ @Test def testTrioCompound = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+ val trio = new Trio("Child_7006504", "Father_7006506", "Mother_7006508")
+
+ trioCompound(record, List(trio))
+ }
+
+ @Test def testDeNovoTrio = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+ val trio = new Trio("Child_7006504", "Father_7006506", "Mother_7006508")
+
+ denovoTrio(record, List(trio))
+ }
+
+ @Test def testInIDSet() = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ inIdSet(record, Set("rs199537431")) shouldBe true
+ inIdSet(record, Set("dummy")) shouldBe false
+ }
+
+}
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..b7a30c52e615c18502646d23b325637e288e8e72
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
@@ -0,0 +1,414 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.{ Files, Paths }
+
+import htsjdk.variant.variantcontext.Allele
+import htsjdk.variant.vcf.VCFFileReader
+import nl.lumc.sasc.biopet.tools.VcfStats._
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.mutable
+
+/**
+ * Test class for [[VcfStats]]
+ *
+ * Created by pjvan_thof on 2/5/15.
+ */
+class VcfStatsTest extends TestNGSuite with Matchers {
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ @Test
+ def testSampleToSampleStats(): Unit = {
+ val s1 = SampleToSampleStats()
+ val s2 = SampleToSampleStats()
+ s1.alleleOverlap shouldBe 0
+ s1.genotypeOverlap shouldBe 0
+ s2.alleleOverlap shouldBe 0
+ s2.genotypeOverlap shouldBe 0
+
+ s1 += s2
+ s1.alleleOverlap shouldBe 0
+ s1.genotypeOverlap shouldBe 0
+ s2.alleleOverlap shouldBe 0
+ s2.genotypeOverlap shouldBe 0
+
+ s2.alleleOverlap = 2
+ s2.genotypeOverlap = 3
+
+ s1 += s2
+ s1.alleleOverlap shouldBe 2
+ s1.genotypeOverlap shouldBe 3
+ s2.alleleOverlap shouldBe 2
+ s2.genotypeOverlap shouldBe 3
+
+ s1 += s2
+ s1.alleleOverlap shouldBe 4
+ s1.genotypeOverlap shouldBe 6
+ s2.alleleOverlap shouldBe 2
+ s2.genotypeOverlap shouldBe 3
+ }
+
+ @Test
+ def testSampleStats(): Unit = {
+ val s1 = SampleStats()
+ val s2 = SampleStats()
+
+ s1.sampleToSample += "s1" -> SampleToSampleStats()
+ s1.sampleToSample += "s2" -> SampleToSampleStats()
+ s2.sampleToSample += "s1" -> SampleToSampleStats()
+ s2.sampleToSample += "s2" -> SampleToSampleStats()
+
+ s1.sampleToSample("s1").alleleOverlap = 1
+ s2.sampleToSample("s2").alleleOverlap = 2
+
+ val bla1 = s1.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) += "1" -> mutable.Map(1 -> 1)
+ s1.genotypeStats += "chr" -> bla1
+ val bla2 = s2.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) += "2" -> mutable.Map(2 -> 2)
+ s2.genotypeStats += "chr" -> bla2
+
+ val ss1 = SampleToSampleStats()
+ val ss2 = SampleToSampleStats()
+
+ s1 += s2
+ s1.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) shouldBe mutable.Map("1" -> mutable.Map(1 -> 1), "2" -> mutable.Map(2 -> 2))
+ ss1.alleleOverlap = 1
+ ss2.alleleOverlap = 2
+ s1.sampleToSample shouldBe mutable.Map("s1" -> ss1, "s2" -> ss2)
+
+ s1 += s2
+ s1.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) shouldBe mutable.Map("1" -> mutable.Map(1 -> 1), "2" -> mutable.Map(2 -> 4))
+
+ s1 += s1
+ s1.genotypeStats.getOrElse("chr", mutable.Map[String, mutable.Map[Any, Int]]()) shouldBe mutable.Map("1" -> mutable.Map(1 -> 2), "2" -> mutable.Map(2 -> 8))
+ }
+
+ @Test
+ def testAlleleOverlap(): Unit = {
+
+ val a1 = Allele.create("G")
+ val a2 = Allele.create("A")
+
+ alleleOverlap(List(a1, a1), List(a1, a1)) shouldBe 2
+ alleleOverlap(List(a2, a2), List(a2, a2)) shouldBe 2
+ alleleOverlap(List(a1, a2), List(a1, a2)) shouldBe 2
+ alleleOverlap(List(a1, a2), List(a2, a1)) shouldBe 2
+ alleleOverlap(List(a2, a1), List(a1, a2)) shouldBe 2
+ alleleOverlap(List(a2, a1), List(a2, a1)) shouldBe 2
+
+ alleleOverlap(List(a1, a2), List(a1, a1)) shouldBe 1
+ alleleOverlap(List(a2, a1), List(a1, a1)) shouldBe 1
+ alleleOverlap(List(a1, a1), List(a1, a2)) shouldBe 1
+ alleleOverlap(List(a1, a1), List(a2, a1)) shouldBe 1
+
+ alleleOverlap(List(a1, a1), List(a2, a2)) shouldBe 0
+ alleleOverlap(List(a2, a2), List(a1, a1)) shouldBe 0
+ }
+
+ @Test
+ def testMergeStatsMap = {
+ val m1: mutable.Map[Any, Int] = mutable.Map("a" -> 1)
+ val m2: mutable.Map[Any, Int] = mutable.Map("b" -> 2)
+
+ mergeStatsMap(m1, m2)
+
+ m1 should equal(mutable.Map("a" -> 1, "b" -> 2))
+
+ val m3: mutable.Map[Any, Int] = mutable.Map(1 -> 500)
+ val m4: mutable.Map[Any, Int] = mutable.Map(6 -> 125)
+
+ mergeStatsMap(m3, m4)
+
+ m3 should equal(mutable.Map(1 -> 500, 6 -> 125))
+
+ mergeStatsMap(m1, m3)
+
+ m1 should equal(mutable.Map("a" -> 1, "b" -> 2, 1 -> 500, 6 -> 125))
+ }
+
+ @Test
+ def testMergeNestedStatsMap = {
+ val m1: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map("test" ->
+ mutable.Map("nested" -> mutable.Map("a" -> 1)))
+ val m2: Map[String, Map[String, Map[Any, Int]]] = Map("test" ->
+ Map("nested" -> Map("b" -> 2)))
+
+ mergeNestedStatsMap(m1, m2)
+
+ m1 should equal(mutable.Map("test" -> mutable.Map("nested" -> mutable.Map("a" -> 1, "b" -> 2))))
+
+ val m3: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map("test" ->
+ mutable.Map("nestedd" -> mutable.Map(1 -> 500)))
+ val m4: Map[String, Map[String, Map[Any, Int]]] = Map("test" ->
+ Map("nestedd" -> Map(6 -> 125)))
+
+ mergeNestedStatsMap(m3, m4)
+
+ m3 should equal(mutable.Map("test" -> mutable.Map("nestedd" -> mutable.Map(1 -> 500, 6 -> 125))))
+
+ val m5 = m3.toMap.map(x => x._1 -> x._2.toMap.map(y => y._1 -> y._2.toMap))
+
+ mergeNestedStatsMap(m1, m5)
+
+ m1 should equal(mutable.Map("test" -> mutable.Map("nested" -> mutable.Map("a" -> 1, "b" -> 2),
+ "nestedd" -> mutable.Map(1 -> 500, 6 -> 125))))
+ }
+
+ @Test
+ def testValueOfTsv = {
+ val i = new File(resourcePath("/sample.tsv"))
+
+ valueFromTsv(i, "Sample_ID_1", "library") should be(Some("Lib_ID_1"))
+ valueFromTsv(i, "Sample_ID_2", "library") should be(Some("Lib_ID_2"))
+ valueFromTsv(i, "Sample_ID_1", "bam") should be(Some("MyFirst.bam"))
+ valueFromTsv(i, "Sample_ID_2", "bam") should be(Some("MySecond.bam"))
+ valueFromTsv(i, "Sample_ID_3", "bam") should be(empty)
+ }
+
+ @Test
+ def testMain = {
+ val tmp = Files.createTempDirectory("vcfStats")
+ val vcf = resourcePath("/chrQ.vcf.gz")
+ val ref = resourcePath("/fake_chrQ.fa")
+
+ noException should be thrownBy main(Array("-I", vcf, "-R", ref, "-o", tmp.toAbsolutePath.toString))
+ noException should be thrownBy main(Array("-I", vcf, "-R", ref, "-o", tmp.toAbsolutePath.toString, "--allInfoTags"))
+ noException should be thrownBy main(Array("-I", vcf, "-R", ref, "-o",
+ tmp.toAbsolutePath.toString, "--allInfoTags", "--allGenotypeTags"))
+ noException should be thrownBy main(Array("-I", vcf, "-R", ref, "-o",
+ tmp.toAbsolutePath.toString, "--binSize", "50", "--writeBinStats"))
+ noException should be thrownBy main(Array("-I", vcf, "-R", ref, "-o",
+ tmp.toAbsolutePath.toString, "--binSize", "50", "--writeBinStats",
+ "--generalWiggle", "Total"))
+ noException should be thrownBy main(Array("-I", vcf, "-R", ref, "-o",
+ tmp.toAbsolutePath.toString, "--binSize", "50", "--writeBinStats",
+ "--genotypeWiggle", "Total"))
+
+ val genotypes = List("Het", "HetNonRef", "Hom", "HomRef", "HomVar", "Mixed", "NoCall", "NonInformative",
+ "Available", "Called", "Filtered", "Variant")
+
+ genotypes.foreach(
+ x => noException should be thrownBy main(Array("-I", vcf, "-R", ref, "-o",
+ tmp.toAbsolutePath.toString, "--binSize", "50", "--writeBinStats",
+ "--genotypeWiggle", x))
+ )
+
+ val general = List("Biallelic", "ComplexIndel", "Filtered", "FullyDecoded", "Indel", "Mixed",
+ "MNP", "MonomorphicInSamples", "NotFiltered", "PointEvent", "PolymorphicInSamples",
+ "SimpleDeletion", "SimpleInsertion", "SNP", "StructuralIndel", "Symbolic",
+ "SymbolicOrSV", "Variant")
+
+ general.foreach(
+ x => noException should be thrownBy main(Array("-I", vcf, "-R", ref, "-o",
+ tmp.toAbsolutePath.toString, "--binSize", "50", "--writeBinStats",
+ "--generalWiggle", x))
+ )
+
+ // returns null when validation fails
+ def validateArgs(array: Array[String]): Option[Args] = {
+ val argsParser = new OptParser
+ argsParser.parse(array, Args())
+ }
+
+ val stderr1 = new java.io.ByteArrayOutputStream
+ Console.withErr(stderr1) {
+ validateArgs(Array("-I", vcf, "-R", ref, "-o",
+ tmp.toAbsolutePath.toString, "--binSize", "50", "--writeBinStats",
+ "--genotypeWiggle", "NonexistentThing")) shouldBe empty
+ }
+
+ val stderr2 = new java.io.ByteArrayOutputStream
+ Console.withErr(stderr2) {
+ validateArgs(Array("-I", vcf, "-R", ref, "-o",
+ tmp.toAbsolutePath.toString, "--binSize", "50", "--writeBinStats",
+ "--generalWiggle", "NonexistentThing")) shouldBe empty
+ }
+
+ val stderr3 = new java.io.ByteArrayOutputStream
+ Console.withErr(stderr3) {
+ validateArgs(Array("-R", ref, "-o",
+ tmp.toAbsolutePath.toString)) shouldBe empty
+ }
+ }
+
+ @Test
+ def testSortAnyAny = {
+ //stub
+ val one: Any = 1
+ val two: Any = 2
+ val text: Any = "hello"
+ val text2: Any = "goodbye"
+
+ sortAnyAny(one, two) shouldBe true
+ sortAnyAny(two, one) shouldBe false
+ sortAnyAny(text, text2) shouldBe false
+ sortAnyAny(text2, text) shouldBe true
+ sortAnyAny(one, text) shouldBe true
+ sortAnyAny(text, one) shouldBe false
+ }
+
+ @Test
+ def testCheckGeneral = {
+ val record = new VCFFileReader(new File(resourcePath("/chrQ.vcf.gz"))).iterator().next()
+
+ val blah = checkGeneral(record, List())
+
+ blah.get("chrQ") should not be empty
+ blah.get("total") should not be empty
+
+ val chrq = blah.get("chrQ").get
+ chrq.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
+ chrq.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
+ chrq.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
+ chrq.get("SampleDistribution-Hom") shouldEqual Some(Map(1 -> 1))
+ chrq.get("SampleDistribution-HomRef") shouldEqual Some(Map(1 -> 1))
+ chrq.get("SampleDistribution-Available") shouldEqual Some(Map(3 -> 1))
+ chrq.get("QUAL") shouldEqual Some(Map(1541 -> 1))
+ chrq.get("SampleDistribution-HetNonRef") shouldEqual Some(Map(0 -> 1))
+ chrq.get("SampleDistribution-Het") shouldEqual Some(Map(2 -> 1))
+ chrq.get("SampleDistribution-NoCall") shouldEqual Some(Map(0 -> 1))
+ chrq.get("SampleDistribution-Filtered") shouldEqual Some(Map(0 -> 1))
+ chrq.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1))
+ chrq.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
+
+ chrq.get("general") should not be empty
+ val general = chrq.get("general").get
+
+ general.get("PolymorphicInSamples") shouldEqual Some(1)
+ general.get("ComplexIndel") shouldEqual Some(0)
+ general.get("FullyDecoded") shouldEqual Some(0)
+ general.get("PointEvent") shouldEqual Some(0)
+ general.get("MNP") shouldEqual Some(0)
+ general.get("Indel") shouldEqual Some(1)
+ general.get("Biallelic") shouldEqual Some(1)
+ general.get("SimpleDeletion") shouldEqual Some(0)
+ general.get("Variant") shouldEqual Some(1)
+ general.get("SymbolicOrSV") shouldEqual Some(0)
+ general.get("MonomorphicInSamples") shouldEqual Some(0)
+ general.get("SNP") shouldEqual Some(0)
+ general.get("Filtered") shouldEqual Some(0)
+ general.get("StructuralIndel") shouldEqual Some(0)
+ general.get("Total") shouldEqual Some(1)
+ general.get("Mixed") shouldEqual Some(0)
+ general.get("NotFiltered") shouldEqual Some(1)
+ general.get("Symbolic") shouldEqual Some(0)
+ general.get("SimpleInsertion") shouldEqual Some(1)
+
+ val total = blah.get("total").get
+ total.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
+ total.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
+ total.get("SampleDistribution-Mixed") shouldEqual Some(Map(0 -> 1))
+ total.get("SampleDistribution-Hom") shouldEqual Some(Map(1 -> 1))
+ total.get("SampleDistribution-HomRef") shouldEqual Some(Map(1 -> 1))
+ total.get("SampleDistribution-Available") shouldEqual Some(Map(3 -> 1))
+ total.get("QUAL") shouldEqual Some(Map(1541 -> 1))
+ total.get("SampleDistribution-HetNonRef") shouldEqual Some(Map(0 -> 1))
+ total.get("SampleDistribution-Het") shouldEqual Some(Map(2 -> 1))
+ total.get("SampleDistribution-NoCall") shouldEqual Some(Map(0 -> 1))
+ total.get("SampleDistribution-Filtered") shouldEqual Some(Map(0 -> 1))
+ total.get("SampleDistribution-HomVar") shouldEqual Some(Map(0 -> 1))
+ total.get("SampleDistribution-Variant") shouldEqual Some(Map(2 -> 1))
+
+ chrq.get("general") should not be empty
+ val totGeneral = total.get("general").get
+
+ totGeneral.get("PolymorphicInSamples") shouldEqual Some(1)
+ totGeneral.get("ComplexIndel") shouldEqual Some(0)
+ totGeneral.get("FullyDecoded") shouldEqual Some(0)
+ totGeneral.get("PointEvent") shouldEqual Some(0)
+ totGeneral.get("MNP") shouldEqual Some(0)
+ totGeneral.get("Indel") shouldEqual Some(1)
+ totGeneral.get("Biallelic") shouldEqual Some(1)
+ totGeneral.get("SimpleDeletion") shouldEqual Some(0)
+ totGeneral.get("Variant") shouldEqual Some(1)
+ totGeneral.get("SymbolicOrSV") shouldEqual Some(0)
+ totGeneral.get("MonomorphicInSamples") shouldEqual Some(0)
+ totGeneral.get("SNP") shouldEqual Some(0)
+ totGeneral.get("Filtered") shouldEqual Some(0)
+ totGeneral.get("StructuralIndel") shouldEqual Some(0)
+ totGeneral.get("Total") shouldEqual Some(1)
+ totGeneral.get("Mixed") shouldEqual Some(0)
+ totGeneral.get("NotFiltered") shouldEqual Some(1)
+ totGeneral.get("Symbolic") shouldEqual Some(0)
+ totGeneral.get("SimpleInsertion") shouldEqual Some(1)
+ }
+
+ @Test
+ def testCheckGenotype = {
+ val record = new VCFFileReader(new File(resourcePath("/chrQ.vcf.gz"))).iterator().next()
+
+ val genotype = record.getGenotype(0)
+
+ val blah = checkGenotype(record, genotype, List())
+
+ blah.get("chrQ") should not be empty
+ blah.get("total") should not be empty
+
+ val chrq = blah.get("chrQ").get
+ chrq.get("GQ") shouldEqual Some(Map(99 -> 1))
+ chrq.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
+ chrq.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
+ chrq.get("DP") shouldEqual Some(Map(45 -> 1))
+ chrq.get("AD-alt") shouldEqual Some(Map(21 -> 1))
+ chrq.get("AD-ref") shouldEqual Some(Map(24 -> 1))
+ chrq.get("general") should not be empty
+
+ val general = chrq.get("general").get
+ general.get("Hom") shouldEqual Some(0)
+ general.get("NoCall") shouldEqual Some(0)
+ general.get("Variant") shouldEqual Some(1)
+ general.get("Filtered") shouldEqual Some(0)
+ general.get("NonInformative") shouldEqual Some(0)
+ general.get("Called") shouldEqual Some(1)
+ general.get("Total") shouldEqual Some(1)
+ general.get("HomVar") shouldEqual Some(0)
+ general.get("HomRef") shouldEqual Some(0)
+ general.get("Mixed") shouldEqual Some(0)
+ general.get("Available") shouldEqual Some(1)
+ general.get("Het") shouldEqual Some(1)
+ general.get("HetNonRef") shouldEqual Some(0)
+
+ val total = blah.get("total").get
+ total.get("GQ") shouldEqual Some(Map(99 -> 1))
+ total.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
+ total.get("AD-used") shouldEqual Some(Map(24 -> 1, 21 -> 1))
+ total.get("DP") shouldEqual Some(Map(45 -> 1))
+ total.get("AD-alt") shouldEqual Some(Map(21 -> 1))
+ total.get("AD-ref") shouldEqual Some(Map(24 -> 1))
+ total.get("general") should not be empty
+
+ val totGeneral = total.get("general").get
+ totGeneral.get("Hom") shouldEqual Some(0)
+ totGeneral.get("NoCall") shouldEqual Some(0)
+ totGeneral.get("Variant") shouldEqual Some(1)
+ totGeneral.get("Filtered") shouldEqual Some(0)
+ totGeneral.get("NonInformative") shouldEqual Some(0)
+ totGeneral.get("Called") shouldEqual Some(1)
+ totGeneral.get("Total") shouldEqual Some(1)
+ totGeneral.get("HomVar") shouldEqual Some(0)
+ totGeneral.get("HomRef") shouldEqual Some(0)
+ totGeneral.get("Mixed") shouldEqual Some(0)
+ totGeneral.get("Available") shouldEqual Some(1)
+ totGeneral.get("Het") shouldEqual Some(1)
+ totGeneral.get("HetNonRef") shouldEqual Some(0)
+ }
+}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
diff --git a/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..af8ff6267d5c73dad9eaa10762b1d356a2641626
--- /dev/null
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
@@ -0,0 +1,181 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+import java.util
+
+import htsjdk.variant.vcf.VCFFileReader
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.util.Random
+import scala.collection.JavaConversions._
+
+import nl.lumc.sasc.biopet.utils.VcfUtils.identicalVariantContext
+
+/**
+ * Test class for [[VcfWithVcfTest]]
+ *
+ * Created by ahbbollen on 10-4-15.
+ */
+class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
+ import VcfWithVcf._
+
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val veppedPath = resourcePath("/VEP_oneline.vcf.gz")
+ val unveppedPath = resourcePath("/unvep_online.vcf.gz")
+ val rand = new Random()
+
+ @Test def testOutputTypeVcf() = {
+ val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
+ main(arguments)
+ }
+
+ @Test def testOutputTypeVcfGz() = {
+ val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf.gz").getAbsolutePath
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
+ main(arguments)
+ }
+
+ @Test def testOutputTypeBcf() = {
+ val tmpPath = File.createTempFile("VcfWithVcf_", ".bcf").getAbsolutePath
+ val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
+ main(arguments)
+ }
+
+ @Test def testOutputFieldException = {
+ val tmpPath = File.createTempFile("VCFWithVCf", ".vcf").getAbsolutePath
+ val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:AC")
+ an[IllegalArgumentException] should be thrownBy main(args)
+ val thrown = the[IllegalArgumentException] thrownBy main(args)
+ thrown.getMessage should equal("Field 'AC' already exists in input vcf")
+ }
+
+ @Test def testInputFieldException = {
+ val tmpPath = File.createTempFile("VCFWithVCf", ".vcf").getAbsolutePath
+ val args = Array("-I", unveppedPath, "-s", unveppedPath, "-o", tmpPath, "-f", "CSQ:NEW_CSQ")
+ an[IllegalArgumentException] should be thrownBy main(args)
+ val thrown = the[IllegalArgumentException] thrownBy main(args)
+ thrown.getMessage should equal("Field 'CSQ' does not exist in secondary vcf")
+ }
+
+ @Test def testMinMethodException = {
+ val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+ val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:CSQ:min")
+ an[IllegalArgumentException] should be thrownBy main(args)
+ val thrown = the[IllegalArgumentException] thrownBy main(args)
+ thrown.getMessage should equal("Type of field CSQ is not numeric")
+ }
+
+ @Test def testMaxMethodException = {
+ val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+ val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:CSQ:max")
+ an[IllegalArgumentException] should be thrownBy main(args)
+ val thrown = the[IllegalArgumentException] thrownBy main(args)
+ thrown.getMessage should equal("Type of field CSQ is not numeric")
+ }
+
+ @Test
+ def testFieldMap = {
+ val unvep_record = new VCFFileReader(new File(unveppedPath)).iterator().next()
+
+ var fields = List(new Fields("FG", "FG"))
+ fields :::= List(new Fields("FD", "FD"))
+ fields :::= List(new Fields("GM", "GM"))
+ fields :::= List(new Fields("GL", "GL"))
+ fields :::= List(new Fields("CP", "CP"))
+ fields :::= List(new Fields("CG", "CG"))
+ fields :::= List(new Fields("CN", "CN"))
+ fields :::= List(new Fields("DSP", "DSP"))
+ fields :::= List(new Fields("AC", "AC"))
+ fields :::= List(new Fields("AF", "AF"))
+ fields :::= List(new Fields("AN", "AN"))
+ fields :::= List(new Fields("BaseQRankSum", "BaseQRankSum"))
+ fields :::= List(new Fields("DP", "DP"))
+ fields :::= List(new Fields("FS", "FS"))
+ fields :::= List(new Fields("MLEAC", "MLEAC"))
+ fields :::= List(new Fields("MLEAF", "MLEAF"))
+ fields :::= List(new Fields("MQ", "MQ"))
+ fields :::= List(new Fields("MQ0", "MQ0"))
+ fields :::= List(new Fields("MQRankSum", "MQRankSum"))
+ fields :::= List(new Fields("QD", "QD"))
+ fields :::= List(new Fields("RPA", "RPA"))
+ fields :::= List(new Fields("RU", "RU"))
+ fields :::= List(new Fields("ReadPosRankSum", "ReadPosRankSum"))
+ fields :::= List(new Fields("VQSLOD", "VQSLOD"))
+ fields :::= List(new Fields("culprit", "culprit"))
+
+ val fieldMap = createFieldMap(fields, List(unvep_record))
+
+ fieldMap("FG") shouldBe List("intron")
+ fieldMap("FD") shouldBe List("unknown")
+ fieldMap("GM") shouldBe List("NM_152486.2")
+ fieldMap("GL") shouldBe List("SAMD11")
+ fieldMap("CP") shouldBe List("0.000")
+ fieldMap("CG") shouldBe List("-1.630")
+ fieldMap("CN") shouldBe List("2294", "3274", "30362", "112930")
+ fieldMap("DSP") shouldBe List("107")
+ fieldMap("AC") shouldBe List("2")
+ fieldMap("AF") shouldBe List("0.333")
+ fieldMap("AN") shouldBe List("6")
+ fieldMap("DP") shouldBe List("124")
+ fieldMap("FS") shouldBe List("1.322")
+ fieldMap("MLEAC") shouldBe List("2")
+ fieldMap("MLEAF") shouldBe List("0.333")
+ fieldMap("MQ") shouldBe List("60.0")
+ fieldMap("MQ0") shouldBe List("0")
+ fieldMap("MQRankSum") shouldBe List("-0.197")
+ fieldMap("QD") shouldBe List("19.03")
+ fieldMap("RPA") shouldBe List("1", "2")
+ fieldMap("RU") shouldBe List("A")
+ fieldMap("ReadPosRankSum") shouldBe List("-0.424")
+ fieldMap("VQSLOD") shouldBe List("0.079")
+ fieldMap("culprit") shouldBe List("FS")
+
+ }
+
+ @Test def testGetSecondaryRecords = {
+ val unvep_record = new VCFFileReader(new File(unveppedPath)).iterator().next()
+ val vep_reader = new VCFFileReader(new File(veppedPath))
+ val vep_record = vep_reader.iterator().next()
+
+ val secRec = getSecondaryRecords(vep_reader, unvep_record, false)
+
+ secRec.foreach(x => identicalVariantContext(x, vep_record) shouldBe true)
+ }
+
+ @Test def testCreateRecord = {
+ val unvep_record = new VCFFileReader(new File(unveppedPath)).iterator().next()
+ val vep_reader = new VCFFileReader(new File(veppedPath))
+ val header = vep_reader.getFileHeader
+ val vep_record = vep_reader.iterator().next()
+
+ val secRec = getSecondaryRecords(vep_reader, unvep_record, false)
+
+ val fieldMap = createFieldMap(List(new Fields("CSQ", "CSQ")), secRec)
+ val created_record = createRecord(fieldMap, unvep_record, List(new Fields("CSQ", "CSQ")), header)
+ identicalVariantContext(created_record, vep_record) shouldBe true
+ }
+
+}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
similarity index 89%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
index b2a063f9853c07ceb23f623b174e5d7980dc275f..5a12e9b579296b58a2764fdaa0b5b916717e384f 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
@@ -47,37 +47,37 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
val rand = new Random()
@Test def testGzOutputExplode(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf.gz"
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
+ val tmpPath = File.createTempFile("VepNormalizer_", ".vcf.gz").getAbsolutePath
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpPath, "-m", "explode")
main(arguments)
}
@Test def testVcfOutputExplode(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf"
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
+ val tmpPath = File.createTempFile("VepNormalizer_", ".vcf").getAbsolutePath
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpPath, "-m", "explode")
main(arguments)
}
@Test def testBcfOutputExplode(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".bcf"
+ val tmp_path = File.createTempFile("VepNormalizer_", ".bcf").getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
main(arguments)
}
@Test def testGzOutputStandard(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf.gz"
+ val tmp_path = File.createTempFile("VepNormalizer_", ".vcf.gz").getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
main(arguments)
}
@Test def testVcfOutputStandard(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf"
+ val tmp_path = File.createTempFile("VepNormalizer_", ".vcf").getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
main(arguments)
}
@Test def testBcfOutputStandard(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".bcf"
+ val tmp_path = File.createTempFile("VepNormalizer_", ".bcf").getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
main(arguments)
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
diff --git a/public/biopet-utils/pom.xml b/public/biopet-utils/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bb9f2b2611c31ceed8a3e0f6505d4dca2b1198a0
--- /dev/null
+++ b/public/biopet-utils/pom.xml
@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <parent>
+ <artifactId>Biopet</artifactId>
+ <groupId>nl.lumc.sasc</groupId>
+ <version>0.5.0-SNAPSHOT</version>
+ <relativePath>../</relativePath>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+
+ <artifactId>BiopetUtils</artifactId>
+ <packaging>jar</packaging>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>1.9.5</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.10</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ <version>1.2.17</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>2.1</version>
+ </dependency>
+ <dependency>
+ <groupId>com.github.samtools</groupId>
+ <artifactId>htsjdk</artifactId>
+ <version>1.132</version>
+ </dependency>
+ <dependency>
+ <groupId>org.scala-lang</groupId>
+ <artifactId>scala-library</artifactId>
+ <version>2.10.4</version>
+ </dependency>
+ <dependency>
+ <groupId>org.yaml</groupId>
+ <artifactId>snakeyaml</artifactId>
+ <version>1.15</version>
+ </dependency>
+ <dependency>
+ <groupId>io.argonaut</groupId>
+ <artifactId>argonaut_2.10</artifactId>
+ <version>6.1-M4</version>
+ </dependency>
+ <dependency>
+ <groupId>com.github.scopt</groupId>
+ <artifactId>scopt_2.10</artifactId>
+ <version>3.3.0</version>
+ </dependency>
+ </dependencies>
+</project>
\ No newline at end of file
diff --git a/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R b/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
new file mode 100644
index 0000000000000000000000000000000000000000..a1959a262cf868d9949b0320f57c9d54b7c50860
--- /dev/null
+++ b/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotScatter.R
@@ -0,0 +1,40 @@
+library(reshape2)
+library(ggplot2)
+library(argparse)
+
+parser <- ArgumentParser(description='Process some integers')
+parser$add_argument('--input', dest='input', type='character', help='Input tsv file', required=TRUE)
+parser$add_argument('--output', dest='output', type='character', help='Output png file', required=TRUE)
+parser$add_argument('--width', dest='width', type='integer', default = 500)
+parser$add_argument('--height', dest='height', type='integer', default = 500)
+parser$add_argument('--xlabel', dest='xlabel', type='character')
+parser$add_argument('--ylabel', dest='ylabel', type='character', required=TRUE)
+parser$add_argument('--llabel', dest='llabel', type='character')
+parser$add_argument('--title', dest='title', type='character')
+parser$add_argument('--removeZero', dest='removeZero', type='character', default="false")
+
+arguments <- parser$parse_args()
+
+png(filename = arguments$output, width = arguments$width, height = arguments$height)
+
+DF <- read.table(arguments$input, header=TRUE)
+
+if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
+
+colnames(DF)[1] <- "Rank"
+
+DF1 <- melt(DF, id.var="Rank")
+
+if (arguments$removeZero == "true") DF1 <- DF1[DF1$value > 0, ]
+if (arguments$removeZero == "true") print("Removed 0 values")
+
+ggplot(DF1, aes(x = Rank, y = value, group = variable, color = variable)) +
+ xlab(xlab) +
+ ylab(arguments$ylabel) +
+ guides(fill=guide_legend(title=arguments$llabel)) +
+ theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
+ ggtitle(arguments$title) +
+ theme_bw() +
+ geom_point()
+
+dev.off()
diff --git a/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R b/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
new file mode 100644
index 0000000000000000000000000000000000000000..eee20c030b280c9246ce77428d3415173ea1b796
--- /dev/null
+++ b/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R
@@ -0,0 +1,40 @@
+library(reshape2)
+library(ggplot2)
+library(argparse)
+
+parser <- ArgumentParser(description='Process some integers')
+parser$add_argument('--input', dest='input', type='character', help='Input tsv file', required=TRUE)
+parser$add_argument('--output', dest='output', type='character', help='Output png file', required=TRUE)
+parser$add_argument('--width', dest='width', type='integer', default = 500)
+parser$add_argument('--height', dest='height', type='integer', default = 500)
+parser$add_argument('--xlabel', dest='xlabel', type='character')
+parser$add_argument('--ylabel', dest='ylabel', type='character', required=TRUE)
+parser$add_argument('--llabel', dest='llabel', type='character')
+parser$add_argument('--title', dest='title', type='character')
+parser$add_argument('--removeZero', dest='removeZero', type='character', default="false")
+
+arguments <- parser$parse_args()
+
+png(filename = arguments$output, width = arguments$width, height = arguments$height)
+
+DF <- read.table(arguments$input, header=TRUE)
+
+if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
+
+colnames(DF)[1] <- "Rank"
+
+DF1 <- melt(DF, id.var="Rank")
+
+if (arguments$removeZero == "true") DF1 <- DF1[DF1$value > 0, ]
+if (arguments$removeZero == "true") print("Removed 0 values")
+
+ggplot(DF1, aes(x = Rank, y = value, group = variable, color = variable)) +
+ xlab(xlab) +
+ ylab(arguments$ylabel) +
+ guides(fill=guide_legend(title=arguments$llabel)) +
+ theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
+ ggtitle(arguments$title) +
+ theme_bw() +
+ geom_line()
+
+dev.off()
diff --git a/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R b/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
new file mode 100644
index 0000000000000000000000000000000000000000..0ae7f942cc69d1047ab2a642342381d5e8f2eade
--- /dev/null
+++ b/public/biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/stackedBar.R
@@ -0,0 +1,35 @@
+library(reshape2)
+library(ggplot2)
+library(argparse)
+
+parser <- ArgumentParser(description='Process some integers')
+parser$add_argument('--input', dest='input', type='character', help='Input tsv file', required=TRUE)
+parser$add_argument('--output', dest='output', type='character', help='Output png file', required=TRUE)
+parser$add_argument('--width', dest='width', type='integer', default = 500)
+parser$add_argument('--height', dest='height', type='integer', default = 500)
+parser$add_argument('--xlabel', dest='xlabel', type='character')
+parser$add_argument('--ylabel', dest='ylabel', type='character', required=TRUE)
+parser$add_argument('--llabel', dest='llabel', type='character')
+parser$add_argument('--title', dest='title', type='character')
+
+arguments <- parser$parse_args()
+
+png(filename = arguments$output, width = arguments$width, height = arguments$height)
+
+DF <- read.table(arguments$input, header=TRUE)
+
+if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
+
+colnames(DF)[1] <- "Rank"
+
+DF1 <- melt(DF, id.var="Rank")
+
+ggplot(DF1, aes(x = Rank, y = value, fill = variable)) +
+ xlab(xlab) +
+ ylab(arguments$ylabel) +
+ guides(fill=guide_legend(title=arguments$llabel)) +
+ theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
+ geom_bar(stat = "identity", width=1) +
+ ggtitle(arguments$title)
+
+dev.off()
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/package.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/package.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/package.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/package.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.scala
index 749ac33a2176ac7b2d6e78e0ca2bb33c85c61877..43522e36dbe93abe174483953caa343b67ca572b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.scala
@@ -13,11 +13,10 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet.utils
import java.io.{ PrintWriter, StringWriter }
-import nl.lumc.sasc.biopet.core.BiopetExecutable._
import nl.lumc.sasc.biopet.{ FullVersion, LastCommitHash }
import org.apache.log4j.Logger
@@ -88,7 +87,7 @@ trait BiopetExecutable extends Logging {
case Array("version") =>
println("version: " + FullVersion)
case Array("license") =>
- println(getLicense)
+ println(BiopetExecutable.getLicense)
case Array(module, name, passArgs @ _*) =>
try {
getCommand(module, name).main(passArgs.toArray)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index 6c1795f48acaecac0dabb01c75238bc1f8ffca13..6a1a0889b68811ae40c3028f706eb3ceda9918fc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
@@ -19,8 +19,7 @@ import java.io.File
import argonaut.Argonaut._
import argonaut._
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, Logging }
-import nl.lumc.sasc.biopet.core.config.ConfigValue
+import nl.lumc.sasc.biopet.utils.config.ConfigValue
import org.yaml.snakeyaml.Yaml
import scala.collection.JavaConversions._
@@ -316,7 +315,7 @@ object ConfigUtils extends Logging {
private def requiredValue(value: ConfigValue): Boolean = {
val exist = valueExists(value)
if (!exist)
- BiopetQScript.addError("Value does not exist but is required, key: " + value.requestIndex.key +
+ Logging.addError("Value does not exist but is required, key: " + value.requestIndex.key +
" module: " + value.requestIndex.module,
if (value.requestIndex.path != Nil) " path: " + value.requestIndex.path.mkString("->") else null)
exist
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
new file mode 100644
index 0000000000000000000000000000000000000000..93a43e273f1a8aa0be87fc9fe3eeb44e9c0b9067
--- /dev/null
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
@@ -0,0 +1,61 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.utils
+
+import org.apache.log4j.Logger
+
+import scala.collection.mutable.ListBuffer
+
+/**
+ * Trait to implement logger function on local class/object
+ */
+trait Logging {
+ /**
+ *
+ * @return Global biopet logger
+ */
+ def logger = Logging.logger
+}
+
+/**
+ * Logger object, has a global logger
+ */
+object Logging {
+ val logger = Logger.getRootLogger
+
+ private val errors: ListBuffer[Exception] = ListBuffer()
+
+ def addError(error: String, debug: String = null): Unit = {
+ val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
+ errors.append(new Exception(msg))
+ }
+
+ def checkErrors(): Unit = {
+ if (errors.nonEmpty) {
+ logger.error("*************************")
+ logger.error("Biopet found some errors:")
+ if (logger.isDebugEnabled) {
+ for (e <- errors) {
+ logger.error(e.getMessage)
+ logger.debug(e.getStackTrace.mkString("Stack trace:\n", "\n", "\n"))
+ }
+ } else {
+ errors.map(_.getMessage).sorted.distinct.foreach(logger.error(_))
+ }
+ throw new IllegalStateException("Biopet found errors")
+ }
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/MainCommand.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/MainCommand.scala
index cdd226c89f6f2363a452e98116d60b691c1033c1..9a8550d9be1293c1dd8afa02bfe75c7b7d9793e2 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/MainCommand.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet.utils
/**
* This trait is used in the biopet executable
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ToolCommand.scala
similarity index 92%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ToolCommand.scala
index 68451bc26139618b987552ba05766aa512497ec0..ce2f099b25077e0caecd3edc4e674ced64349069 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ToolCommand.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core
+package nl.lumc.sasc.biopet.utils
import nl.lumc.sasc.biopet.FullVersion
@@ -54,6 +54,3 @@ trait ToolCommand extends MainCommand with Logging {
protected type OptParser <: AbstractOptParser
}
-trait ToolCommandFuntion extends BiopetJavaCommandLineFunction {
- override def getVersion = Some("Biopet " + FullVersion)
-}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
similarity index 54%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
index 9074ff1f3bcc71fda5ad5c8aa9ba5ae5867fc6c8..8e375f4e7e35cbb49c9cc90c688753b2b6ca42ea 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
@@ -15,6 +15,8 @@
*/
package nl.lumc.sasc.biopet.utils
+import java.util
+
import htsjdk.variant.variantcontext.VariantContext
import scala.collection.JavaConversions._
@@ -43,4 +45,39 @@ object VcfUtils {
def fillAllele(bases: String, newSize: Int, fillWith: Char = '-'): String = {
bases + Array.fill[Char](newSize - bases.length)(fillWith).mkString
}
+
+ /**
+ * Stands for scalaListToJavaObjectArrayList
+ * Convert a scala List[Any] to a java ArrayList[Object]. This is necessary for BCF conversions
+ * As scala ints and floats cannot be directly cast to java objects (they aren't objects),
+ * we need to box them.
+ * For items not Int, Float or Object, we assume them to be strings (TODO: sane assumption?)
+ * @param array scala List[Any]
+ * @return converted java ArrayList[Object]
+ */
+ def scalaListToJavaObjectArrayList(array: List[Any]): util.ArrayList[Object] = {
+ val out = new util.ArrayList[Object]()
+
+ array.foreach {
+ case x: Long => out.add(Long.box(x))
+ case x: Int => out.add(Int.box(x))
+ case x: Char => out.add(Char.box(x))
+ case x: Byte => out.add(Byte.box(x))
+ case x: Double => out.add(Double.box(x))
+ case x: Float => out.add(Float.box(x))
+ case x: Boolean => out.add(Boolean.box(x))
+ case x: String => out.add(x)
+ case x: Object => out.add(x)
+ case x => out.add(x.toString)
+ }
+ out
+ }
+
+ //TODO: Add genotype comparing to this function
+ def identicalVariantContext(var1: VariantContext, var2: VariantContext): Boolean = {
+ var1.getContig == var2.getContig &&
+ var1.getStart == var2.getStart &&
+ var1.getEnd == var2.getEnd &&
+ var1.getAttributes == var2.getAttributes
+ }
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
index 10099c57983b7f0f5af4cf1070b1ed7d6753ac69..1d536084f976312300c091744a99a01a4ae4c3e3 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
@@ -13,12 +13,10 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core.config
+package nl.lumc.sasc.biopet.utils.config
import java.io.{ File, PrintWriter }
-
-import nl.lumc.sasc.biopet.core.Logging
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
import nl.lumc.sasc.biopet.utils.ConfigUtils._
/**
@@ -27,7 +25,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils._
* @constructor Load config with existing map
*/
class Config(var map: Map[String, Any],
- protected[core] var defaults: Map[String, Any] = Map()) extends Logging {
+ protected[config] var defaults: Map[String, Any] = Map()) extends Logging {
logger.debug("Init phase of config")
/** Default constructor */
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValue.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValue.scala
index 1dc4b4702f894f426c56a6d0e7439d7140f1dc25..a4eea343a86dd8a097522825ecd6a8e9d7ecc852 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValue.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValue.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core.config
+package nl.lumc.sasc.biopet.utils.config
import java.io.File
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueIndex.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueIndex.scala
index b310e8b552d2172d9144923efec6fc37c17fe2d7..9bb4340345d0b4aa566d1d35158985d6e76214cf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/ConfigValueIndex.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueIndex.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core.config
+package nl.lumc.sasc.biopet.utils.config
/**
* General case class used as index config values. This stores the path to the value, the module, name of the value and if freeVar is allowed
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
similarity index 96%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
index 6b9c1f922cf398be1c05f2127e978fa315a65aa9..476c4c4435290a9229bc926695cb9153d996d75a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core.config
+package nl.lumc.sasc.biopet.utils.config
import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
@@ -29,10 +29,10 @@ trait Configurable extends ImplicitConversions {
def configPath: List[String] = if (root != null) root.configFullPath else Nil
/** Gets name of module for config */
- protected[core] def configName = getClass.getSimpleName.toLowerCase
+ def configName = getClass.getSimpleName.toLowerCase
/** ull path with module in there */
- protected[core] def configFullPath: List[String] = configPath ::: configName :: Nil
+ def configFullPath: List[String] = configPath ::: configName :: Nil
/** Map to store defaults for config */
def defaults: Map[String, Any] = {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
similarity index 99%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
index c03c4bccc9e22b0b103e032910ea4338fdc3ed42..56b2f303b0a7161879ea9ae01eaf3ba1cc0b86f7 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordList.scala
@@ -9,7 +9,7 @@ import scala.collection.JavaConversions._
import scala.collection.mutable
import scala.collection.mutable.ListBuffer
import scala.io.Source
-import nl.lumc.sasc.biopet.core.Logging
+import nl.lumc.sasc.biopet.utils.Logging
/**
* Created by pjvan_thof on 8/20/15.
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
similarity index 100%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
similarity index 65%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
index 5affda2f871ad8f2e2f20e91a1649a76fa9867f9..fb0e2f0a0706a56c6063c2a2fa2dc199bfee573c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala
@@ -13,26 +13,22 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.rscript
+package nl.lumc.sasc.biopet.utils.rscript
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Extension for en general line plot with R
*
* Created by pjvan_thof on 4/29/15.
*/
-class LinePlot(val root: Configurable) extends RscriptCommandLineFunction {
+class LinePlot(val root: Configurable) extends Rscript {
protected var script: File = config("script", default = "plotXY.R")
- @Input
var input: File = _
- @Output
var output: File = _
var width: Option[Int] = config("width")
@@ -43,14 +39,14 @@ class LinePlot(val root: Configurable) extends RscriptCommandLineFunction {
var title: Option[String] = config("title")
var removeZero: Boolean = config("removeZero", default = false)
- override def cmdLine: String = super.cmdLine +
- required("--input", input) +
- required("--output", output) +
- optional("--width", width) +
- optional("--height", height) +
- optional("--xlabel", xlabel) +
- required("--ylabel", ylabel) +
- optional("--llabel", llabel) +
- optional("--title", title) +
- optional("--removeZero", removeZero)
+ override def cmd = super.cmd ++
+ Seq("--input", input.getAbsolutePath) ++
+ Seq("--output", output.getAbsolutePath) ++
+ width.map(x => Seq("--width", x.toString)).getOrElse(Seq()) ++
+ height.map(x => Seq("--height", x.toString)).getOrElse(Seq()) ++
+ xlabel.map(Seq("--xlabel", _)).getOrElse(Seq()) ++
+ ylabel.map(Seq("--ylabel", _)).getOrElse(Seq()) ++
+ llabel.map(Seq("--llabel", _)).getOrElse(Seq()) ++
+ title.map(Seq("--title", _)).getOrElse(Seq()) ++
+ (if (removeZero) Seq("--removeZero") else Seq())
}
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
new file mode 100644
index 0000000000000000000000000000000000000000..685108d0cb7f31cebfcc4b998017ae0a4c91726f
--- /dev/null
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
@@ -0,0 +1,65 @@
+package nl.lumc.sasc.biopet.utils.rscript
+
+import java.io.{ File, FileOutputStream }
+
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+import scala.sys.process.{ Process, ProcessLogger }
+
+/**
+ * Created by pjvanthof on 13/09/15.
+ */
+trait Rscript extends Configurable {
+ protected var script: File
+
+ def rscriptExecutable: String = config("exe", default = "Rscript", submodule = "Rscript")
+
+ /** This is the defaul implementation, to add arguments override this */
+ def cmd: Seq[String] = Seq(rscriptExecutable, script.getAbsolutePath)
+
+ /**
+ * If script not exist in file system it try to copy it from the jar
+ * @param dir Directory to store temp script, if None or not given File.createTempFile is called
+ */
+ protected def checkScript(dir: Option[File] = None): Unit = {
+ if (script.exists()) {
+ script = script.getAbsoluteFile
+ } else {
+ val rScript: File = dir match {
+ case Some(dir) => new File(dir, script.getName)
+ case _ => File.createTempFile(script.getName, ".R")
+ }
+ if (!rScript.getParentFile.exists) rScript.getParentFile.mkdirs
+
+ val is = getClass.getResourceAsStream(script.getPath)
+ val os = new FileOutputStream(rScript)
+
+ org.apache.commons.io.IOUtils.copy(is, os)
+ os.close()
+
+ script = rScript
+ }
+ }
+
+ /**
+ * Execute rscript on local system
+ * @param logger How to handle stdout and stderr
+ */
+ def runLocal(logger: ProcessLogger): Unit = {
+ checkScript()
+
+ Logging.logger.info("Running: " + cmd.mkString(" "))
+
+ val process = Process(cmd).run(logger)
+ Logging.logger.info(process.exitValue())
+ }
+
+ /**
+ * Execute rscript on local system
+ * Stdout and stderr will go to biopet logger
+ */
+ def runLocal(): Unit = {
+ runLocal(ProcessLogger(Logging.logger.info(_)))
+ }
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/ScatterPlot.scala
similarity index 65%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/ScatterPlot.scala
index f4cccdda176fb1adc09669b2caae155b981265fe..9bcbaffcc7d159cc7e82e012c218d0a2f26fc745 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/ScatterPlot.scala
@@ -13,26 +13,22 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.rscript
+package nl.lumc.sasc.biopet.utils.rscript
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Extension for en general line plot with R
*
* Created by pjvan_thof on 4/29/15.
*/
-class ScatterPlot(val root: Configurable) extends RscriptCommandLineFunction {
+class ScatterPlot(val root: Configurable) extends Rscript {
protected var script: File = config("script", default = "plotScatter.R")
- @Input
var input: File = _
- @Output
var output: File = _
var width: Option[Int] = config("width")
@@ -43,14 +39,14 @@ class ScatterPlot(val root: Configurable) extends RscriptCommandLineFunction {
var title: Option[String] = config("title")
var removeZero: Boolean = config("removeZero", default = false)
- override def cmdLine: String = super.cmdLine +
- required("--input", input) +
- required("--output", output) +
- optional("--width", width) +
- optional("--height", height) +
- optional("--xlabel", xlabel) +
- required("--ylabel", ylabel) +
- optional("--llabel", llabel) +
- optional("--title", title) +
- optional("--removeZero", removeZero)
+ override def cmd = super.cmd ++
+ Seq("--input", input.getAbsolutePath) ++
+ Seq("--output", output.getAbsolutePath) ++
+ width.map(x => Seq("--width", x.toString)).getOrElse(Seq()) ++
+ height.map(x => Seq("--height", x.toString)).getOrElse(Seq()) ++
+ xlabel.map(Seq("--xlabel", _)).getOrElse(Seq()) ++
+ ylabel.map(Seq("--ylabel", _)).getOrElse(Seq()) ++
+ llabel.map(Seq("--llabel", _)).getOrElse(Seq()) ++
+ title.map(Seq("--title", _)).getOrElse(Seq()) ++
+ (if (removeZero) Seq("--removeZero") else Seq())
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
similarity index 65%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
index 4f90a4dbcb1baf293b592ecc4deb445419540587..1965e0a54c810a758db3147de2d24ba8162051fe 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/StackedBarPlot.scala
@@ -13,26 +13,22 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions.rscript
+package nl.lumc.sasc.biopet.utils.rscript
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Extension for en general stackedbar plot with R
*
* Created by pjvan_thof on 4/29/15.
*/
-class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction {
+class StackedBarPlot(val root: Configurable) extends Rscript {
protected var script: File = config("script", default = "stackedBar.R")
- @Input
var input: File = _
- @Output
var output: File = _
var width: Option[Int] = config("width")
@@ -42,13 +38,13 @@ class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction
var llabel: Option[String] = config("llabel")
var title: Option[String] = config("title")
- override def cmdLine: String = super.cmdLine +
- required("--input", input) +
- required("--output", output) +
- optional("--width", width) +
- optional("--height", height) +
- optional("--xlabel", xlabel) +
- required("--ylabel", ylabel) +
- optional("--llabel", llabel) +
- optional("--title", title)
+ override def cmd = super.cmd ++
+ Seq("--input", input.getAbsolutePath) ++
+ Seq("--output", output.getAbsolutePath) ++
+ width.map(x => Seq("--width", x.toString)).getOrElse(Seq()) ++
+ height.map(x => Seq("--height", x.toString)).getOrElse(Seq()) ++
+ xlabel.map(Seq("--xlabel", _)).getOrElse(Seq()) ++
+ ylabel.map(Seq("--ylabel", _)).getOrElse(Seq()) ++
+ llabel.map(Seq("--llabel", _)).getOrElse(Seq()) ++
+ title.map(Seq("--title", _)).getOrElse(Seq())
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
index 916d51eea6c7efb3d66b14b7b2960e8669118812..6b863f81d16d4f26754ea87ddf5c703f35fd4588 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core.summary
+package nl.lumc.sasc.biopet.utils.summary
import java.io.File
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
similarity index 78%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
rename to public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
index 154fd50cff2741501b46c1601db65b38621f196a..371abc9a701e9ed9d224a60bd40df3bcfb8a06cf 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
@@ -1,19 +1,4 @@
-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project that are
- * not part of GATK Queue is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.core.summary
+package nl.lumc.sasc.biopet.utils.summary
/**
* This case class is used for easy access and calculations on those values
@@ -79,4 +64,3 @@ case class SummaryValue(value: Option[Any]) {
}
}
}
-
diff --git a/public/biopet-utils/src/test/resources/log4j.properties b/public/biopet-utils/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/biopet-utils/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
similarity index 99%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
index 571e9d62f0d4eb2ec505c2905e95910472dfda64..ad8ff00ee2e8a09026168efbf99f5926b4583c50 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+++ b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
@@ -19,7 +19,7 @@ import java.io.{ File, PrintWriter }
import argonaut.Argonaut._
import argonaut.Json
-import nl.lumc.sasc.biopet.core.config.{ ConfigValue, ConfigValueIndex }
+import nl.lumc.sasc.biopet.utils.config.{ ConfigValue, ConfigValueIndex }
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
similarity index 99%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
index 023b6db5f17e9d763c2fbd90fee063a5293b27ad..6c92d45d8ff9b594d65af3ba33911ede1718e231 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+++ b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigTest.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core.config
+package nl.lumc.sasc.biopet.utils.config
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, ConfigUtilsTest }
import org.scalatest.Matchers
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
similarity index 97%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
index a09b074bc5792852d75f1623efaf183c8729484e..d0fce8573dd28b45259d3920d3f72ded84508fc2 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
+++ b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigValueTest.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core.config
+package nl.lumc.sasc.biopet.utils.config
import java.io.File
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
similarity index 98%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
index b889f08273eb2617a1af73ba4c2d9f5e4be3b4e7..8853a1183870f304c3529c43c569365c33437a27 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+++ b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.core.config
+package nl.lumc.sasc.biopet.utils.config
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordListTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala
rename to public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecordTest.scala
diff --git a/public/carp/pom.xml b/public/carp/pom.xml
index 58a30235cfe8f84a133d3c88f9185db03cd84e46..6436a278cc101d9914dfbfdc3b8ef74185e85f23 100644
--- a/public/carp/pom.xml
+++ b/public/carp/pom.xml
@@ -35,7 +35,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/public/carp/src/main/resources/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp b/public/carp/src/main/resources/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp
index d6052e8c30de00be49bb0a2e31afeaae99d1513b..d27d719622c39812a9787a4935808c5da55cdd97 100644
--- a/public/carp/src/main/resources/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp
+++ b/public/carp/src/main/resources/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
<%@ var summary: Summary %>
<table class="table">
<tbody>
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index aada3bc2f7c82ec87a14c7acffa4c7cb71c8203b..fcb9aa3e6c5572858609d7c34d6d7a220c739f5e 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.carp
import java.io.File
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.utils.config._
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
index 0a25aaa1c65dca1a6304e217eb6d254b7d7d0e65..c5f2256b0c4cf7c4815c305bab8907573449c5a4 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.carp
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
diff --git a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
index 661aa78a459f5debd38b917f92fd6da349c42dde..c361908fa1110ef7133639e91912acab5cce0da9 100644
--- a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+++ b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.carp
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
diff --git a/public/flexiprep/pom.xml b/public/flexiprep/pom.xml
index bc8f306b3b9ca010e4b41805f30845a11c9c2d87..60077ccf28c406b7358d247edffb101f2c092c9c 100644
--- a/public/flexiprep/pom.xml
+++ b/public/flexiprep/pom.xml
@@ -35,7 +35,12 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
index 23592e9d2fa8fa72f8a28c2daa6a5c8cb318549e..c327a7cef9b16719f1ec4be35ee556005c9bee2e 100644
--- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp
index b28ae9049e4920ca113e0cae2f73cb08f070c94a..0ad776bd7cd861d02b3e8be11b9fa9dad6234008 100644
--- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(java.io.File)
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
index 1eadda6d44c2f6befd49767896d9c260a3ec7658..006388f6bae5570e4f7ec4bcabca5a5439f9e95b 100644
--- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp
index 0ecc838cc733dd80d04455060071e6295246175e..dc0ee78a3334c19eb30733bb76e0d97b73c789d8 100644
--- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp
index 3807e6c8790c21948927f3e25323d59bc620eee0..f91ba1ea26cadc287ec469a6d4205d7aa6ad5c5e 100644
--- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
index 1ec4e7c61d35fbc33fddbfdbd759d71ae1dc38a2..17065bb987d62f147e76a3c096f3db0847bcd265 100644
--- a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
index 5e8936c8a3b7eeaf927113db93eebd63dbecb708..63301b52ad02ad124ac820e791a1de4d385505d3 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.Ln
import scala.collection.mutable
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 0075eb7c5e4350ab93a46f06cfd5faf95246efd0..60fe0da7fbdf0f2ac24ee08bd929c7b66bdaf164 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.{ File, FileNotFoundException }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.Output
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 199b10e7339218ba7761ad7ecf25691d72329dc3..16362f9e1ee2010b549ff82728934330f85925cd 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -15,11 +15,11 @@
*/
package nl.lumc.sasc.biopet.pipelines.flexiprep
-import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
+import nl.lumc.sasc.biopet.extensions.{ Pbzip2, Zcat, Gzip, Sickle }
+import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
index ab8846bc1ea091a1abded962181e63d49af3adb2..c4988cd1e1b131a98d2d4dc52086fef58085e1bc 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
-import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
-import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
+import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
+import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
class FlexiprepReport(val root: Configurable) extends ReportBuilderExtension {
val builder = FlexiprepReport
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
index a6aeac90951fbf0e52b1a1fe283a3a5a625c8306..2105a3c4a2dbc1d2a563c35a6b5e92d752bbefeb 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.Ln
class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq(root) {
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
index 8f2abe9a070cc2a986b93cbfcd5777a83cf9abaa..2cb3f0e7b36175d9bf7633d7d639e6b03612976f 100644
--- a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -18,9 +18,9 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.{ Gzip, Sickle, Zcat }
-import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
diff --git a/public/gears/pom.xml b/public/gears/pom.xml
index 44b9893b6db8b88ecf5c5f96347ff03b95ca9abf..8d09f66d1528a295e18ef5467f2ebd3fa99d8657 100644
--- a/public/gears/pom.xml
+++ b/public/gears/pom.xml
@@ -32,7 +32,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index 0e14359fd649a6d1d56ec5c3aea23fc53f1cbec7..c630b0b3e2d13e4c31466da08d984e6269e18d65 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -16,16 +16,15 @@
package nl.lumc.sasc.biopet.pipelines.gears
import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.FullVersion
import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, SamToFastq }
import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import nl.lumc.sasc.biopet.tools.FastqSync
+import nl.lumc.sasc.biopet.extensions.tools.FastqSync
import org.broadinstitute.gatk.queue.QScript
import scala.collection.JavaConversions._
diff --git a/public/gentrap/pom.xml b/public/gentrap/pom.xml
index fc9cde958323df7761e9e98816120603da82a125..44da56eaf57596f6999276e183f1e1808f9d26b6 100644
--- a/public/gentrap/pom.xml
+++ b/public/gentrap/pom.xml
@@ -33,11 +33,6 @@
<name>Gentrap</name>
<dependencies>
- <dependency>
- <groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
- <version>${project.version}</version>
- </dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId>
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp
index 89d46c7d307ba6839d3eaa40e462764dc12af67a..c1ceb9da2a57464f9b2efe7ecc0ff21b6961c813 100644
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
<%@ var summary: Summary %>
<table class="table">
<tbody>
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 6c3b20c069d742628d10767980b4ea341471411a..c500757088d3c313190cb4a9b0eca65bfc48f9a4 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -19,7 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.FullVersion
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.utils.config._
import nl.lumc.sasc.biopet.core.summary._
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
@@ -29,7 +29,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{ CustomVarScan, Pdflatex, RawBaseCounter }
import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.{ AggrBaseCount, PdfReportTemplateWriter, PlotHeatmap }
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import nl.lumc.sasc.biopet.tools.{ MergeTables, WipeReads }
+import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.queue.function.QFunction
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
index 369b7c6f1ab3d64cbc721df53f6ecad03db20f96..6bf57ea655f67b5ecbc919d4d5f4bd44153dccd7 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
index 1314e5f14537fd1ebcafe5fbc46405e4768d810e..1ce8465cae9c75dbcbed9c85374074202ff9b393 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
@@ -18,10 +18,11 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.extensions.varscan.Mpileup2cns
-import nl.lumc.sasc.biopet.extensions.{ Bgzip, PythonCommandLineFunction, Tabix }
+import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Ad-hoc extension for VarScan variant calling that involves 6-command pipe */
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/Pdflatex.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/Pdflatex.scala
index be9c5b8bbe5a946ccf7ac6f7e47a3f12de8993e6..4747856d6f58943b33f0407b63c37311ab1f67fb 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/Pdflatex.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/Pdflatex.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
index 8bc425dc30d54ffb5aa72ac74d0870275cd88c68..0dfbacd1aaebf7ef74b87a0125407ca29128c9bb 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
@@ -18,8 +18,8 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.language.reflectiveCalls
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
index c0287fd31b4a45b6b0b68ab6b60e5d0dd781ad13..84941f6beeb080c1ffa2b7681eb8bb9e404d6449 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala
index 077e75a96730175830373bb5d524ff2d882536a5..4a8002c9defcf843bfeb6f69b062d68dc6d3b7b6 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
index 6cf247b6ed8b73579fc659d09334ceba7fe81297..eeab93c18279cf3e0510e810ef1199dbb27ee58a 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.{ File, FileOutputStream }
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
index 189fccc05745f37de980bb49ac6f52cefcded4bd..e93049732b32bfe4451fdb6d18a122d070f98c13 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotHeatmap.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
index cee3d7f392f5a622b7aa47bd4d3f8ec1b4d93b25..dd13421069fd331c819653a9fcf2cb4cf3b7c851 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PlotPca.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.scripts
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.RScriptCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 48edf42eeb8ca055fbcc36a01661b2e68e80860d..140db66fd62dd850365b27137cc3df0891bd38a7 100644
--- a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.AggrBaseCount
import nl.lumc.sasc.biopet.utils.ConfigUtils
diff --git a/public/kopisu/pom.xml b/public/kopisu/pom.xml
index 51e9950f579af2cc923ec7419234575f154d9ca6..21f4f0c60dab41cf8d7d7800e8e8ac7654ed6d81 100644
--- a/public/kopisu/pom.xml
+++ b/public/kopisu/pom.xml
@@ -35,7 +35,12 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
index 6c8195968f1c05e2197935a9c279efa80f34289f..7265bee9a1ddeab64cfec191caa9958aa40c2076 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.kopisu
import java.io.File
-import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.utils.config._
import nl.lumc.sasc.biopet.core.{ PipelineCommand, _ }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.conifer.{ ConiferAnalyze, ConiferCall, ConiferRPKM }
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
index 385b211f117dc9bec6d0b756d330422c5e090a4e..6eddbad30c61e741a63687aa1a77df3604017f1a 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.kopisu
import java.io.{ BufferedWriter, File, FileWriter }
import argonaut._
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.function.InProcessFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
diff --git a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
index 5d434c510d5eac56d549d514cd71444a599bea99..9a6f002710a35203f9bff63dff9d776f2c95e246 100644
--- a/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
+++ b/public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.kopisu
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
import org.broadinstitute.gatk.queue.QScript
diff --git a/public/mapping/pom.xml b/public/mapping/pom.xml
index ae181fb48f78b1d36946fee083ae8f6eca0296aa..b5b45bb49c185ff3953a6a1623d154d88d8e7bf6 100644
--- a/public/mapping/pom.xml
+++ b/public/mapping/pom.xml
@@ -35,7 +35,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp b/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
index a8ac1542daca37a7904efa51be3f3521a79fa6ff..84ca1370774a54402d6ae3c01208420df2a64617 100644
--- a/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
+++ b/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
diff --git a/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp b/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp
index d35962f5d53969c6d04700d9c1a76f747bc3b239..41d8249e75c416bebc27a3acff58c1e1498e17ae 100644
--- a/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp
+++ b/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 0932ce18f33b0872f846253152403a225ef4cce1..9d508b12ce727acb0bdfdf52fc485b8e353e5dae 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -19,7 +19,7 @@ import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
-import nl.lumc.sasc.biopet.tools.FastqSplitter
+import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
index ab703e5b5e44a7cc0762e8cff51b1f3b23c66ab9..b2f1b7a846da3483eeed879e493e651f25a83759 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.mapping
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, ReportBuilder }
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
index e9b11906fe59e7ed768a71beab5ce94a3ccaef41..5ca8be2834904e9ebbc68722591a273f36d012ef 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.pipelines.mapping.scripts
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
index 71953da59f9b917d9c28a3a398198a2e823dd82a..849bffcb6998f31e8d527af465de68775b6e11a4 100644
--- a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -18,12 +18,12 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.pipelines.flexiprep.{ Cutadapt, Fastqc, SeqtkSeq }
-import nl.lumc.sasc.biopet.tools.{ FastqSync, SeqStat }
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
diff --git a/public/pom.xml b/public/pom.xml
index 52298c9d81f5ee005e4f75637dd32313c60b9448..cf2ea52f0c710db8abf2ce1c1202a7dd12d80dd0 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -25,7 +25,7 @@
<version>0.5.0-SNAPSHOT</version>
<modules>
- <module>biopet-framework</module>
+ <!--<module>biopet-framework</module>-->
<module>biopet-public-package</module>
<module>bammetrics</module>
<module>flexiprep</module>
@@ -40,6 +40,12 @@
<module>toucan</module>
<module>shiva</module>
<module>basty</module>
+ <module>biopet-core</module>
+ <module>biopet-utils</module>
+ <module>biopet-tools</module>
+ <module>biopet-tools-extensions</module>
+ <module>biopet-extentsions</module>
+ <module>biopet-tools-package</module>
</modules>
<properties>
diff --git a/public/sage/pom.xml b/public/sage/pom.xml
index 83652e23e9f6a7aca2d1e0d3d89f7957542d8430..b88e699a28879de1fd3b92bf60a126006687f440 100644
--- a/public/sage/pom.xml
+++ b/public/sage/pom.xml
@@ -35,7 +35,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index 6affce726fda7045862ac638dac0c56aa8794fa5..4aaee19c295de32dbc306a94cf6fecf63d1ba754 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -15,15 +15,15 @@
*/
package nl.lumc.sasc.biopet.pipelines.sage
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.Cat
import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
import nl.lumc.sasc.biopet.extensions.picard.MergeSamFiles
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
-import nl.lumc.sasc.biopet.tools.SquishBed
-import nl.lumc.sasc.biopet.tools.{ BedtoolsCoverageToCounts, PrefixFastq, SageCountFastq, SageCreateLibrary, SageCreateTagCounts }
+import nl.lumc.sasc.biopet.extensions.tools.SquishBed
+import nl.lumc.sasc.biopet.extensions.tools.{ BedtoolsCoverageToCounts, PrefixFastq, SageCountFastq, SageCreateLibrary, SageCreateTagCounts }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
diff --git a/public/shiva/pom.xml b/public/shiva/pom.xml
index bf08e6111a1689554e20870880aa9b8746c4de54..560818c30c444e703432b9160360c97337931025 100644
--- a/public/shiva/pom.xml
+++ b/public/shiva/pom.xml
@@ -32,7 +32,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp
index bd00a8618bee788821e683ac9c32f6837d3c6464..192cfd2700e8622a24e8c56ac746a7c3f2db4756 100644
--- a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp
+++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
index 91247a368c7194dfbe0ab9cae4073c933e2d21ae..8bc095e84ac3d566d3b0f453ecb0eeccd93f553e 100644
--- a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
+++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.shiva.ShivaReport)
#import(java.io.File)
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
index 4ed090b7cc93d1919acf38924bfbc7c31ce585fc..5721d22515ced92c9102565df158c20be80a2807 100644
--- a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
+++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
@@ -1,4 +1,4 @@
-#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
index 668a01f226a43e8cf087cc575d3dab2ae71f0505..a7d04155b164df95ffad2753ff6a8395f57520c5 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
@@ -16,7 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
index bb5a7f765f69fd9dc7e63c2508f8c476a4b1d076..7e32d72fea38d2e2a2e243604a42438703817946 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report._
-import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
-import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
+import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
+import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
index e370e3b11034df12c5ebce0e90ce4eadae8b1006..79a5219751a35691885b4f61365f4d71b0333105 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
@@ -15,18 +15,16 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva
-import java.io.File
-
import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript, Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.delly.Delly
-import nl.lumc.sasc.biopet.tools.VcfStats
+import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.Input
+
import scala.collection.JavaConversions._
/**
@@ -70,7 +68,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
def biopetScript(): Unit = {
for (cal <- configCallers) {
if (!callersList.exists(_.name == cal))
- BiopetQScript.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
+ Logging.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
}
val callers = callersList.filter(x => configCallers.contains(x.name))
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
index 90b98462ff337c5140f274f64268bd93dd155e7d..d075619c1c39264adf9fba823b043110000b1668 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
@@ -16,7 +16,7 @@
package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index b55597d3f96994b3f6ec3a9fcf79d5f041443f1d..f9cbddd1d75560c3c5e5c538a1ac0080dacd620a 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -18,13 +18,13 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.File
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsCall
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
-import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, VcfStats }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -62,7 +62,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
def biopetScript(): Unit = {
for (cal <- configCallers) {
if (!callersList.exists(_.name == cal))
- BiopetQScript.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
+ Logging.addError("variantcaller '" + cal + "' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
}
val callers = callersList.filter(x => configCallers.contains(x.name)).sortBy(_.prio)
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
index e37756ef76504268f746dfb7ceda62cf29ed2d75..56b6bf172b2d122b2ccd70818d3f9f92161e270d 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam }
-import nl.lumc.sasc.biopet.tools.VcfStats
+import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index 82e21f195aefde3199f19f5a5edf8088ea835201..0281d33f678804d7edd1620d204a0830d4f3201f 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.Freebayes
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter }
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
diff --git a/public/toucan/pom.xml b/public/toucan/pom.xml
index 94dda3da11b6e85b21080bedf2e8147063dd5a9f..ff6f74eba21281d4010925053466265e017f95ee 100644
--- a/public/toucan/pom.xml
+++ b/public/toucan/pom.xml
@@ -35,7 +35,12 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
+ <artifactId>BiopetCore</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index ccd47d551363be2bf65d0fd0176f02f8092060a1..606853f933f6cd1263a0f44193e5ae0e615812df 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
@@ -15,11 +15,11 @@
*/
package nl.lumc.sasc.biopet.pipelines.toucan
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
-import nl.lumc.sasc.biopet.tools.{ VcfWithVcf, VepNormalizer }
+import nl.lumc.sasc.biopet.extensions.tools.{ VcfWithVcf, VepNormalizer }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
rename to public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
index 1939445765451d40f3c8596f04370d21e4c889cd..10795533490ad7f0b696de22a64ca86d54a3492d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.pindel
import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/// Pindel is actually a mini pipeline executing binaries from the pindel package
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
similarity index 97%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
rename to public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index e2d5ce2db18367d259af3c2ee21b1d3c0870acd4..cbe957e79fe1c3e013fb399fe30859e144ae2ed5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.pindel
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
rename to public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
index 4ca3f9e2ca5ea2ea2f791dab2cdd6b577559304a..55127e59f4be2b5e8248bfcffa45ae8cae3ffe5e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.pindel
import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class PindelConfig(val root: Configurable) extends BiopetJavaCommandLineFunction {
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index e6def691af3d699c5087be58d94366bd85ae80d5..a0ade5706206c60d9a1a470002c783d0b98a3590 100644
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -21,7 +21,7 @@ package nl.lumc.sasc.biopet.pipelines.yamsvp
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer