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-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
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 381bfa909538d3effae59e0a8dde8801efb29eb1..49f4e3893b7fe63ff03fca94f030363c54d1217f 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 9d78a353701162e6b3f00b59ac97f6f3cdfcb8df..be479a8fa972fe896fb8d45cd74708944ba4ba64 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 7bcbdca8ed1170f4ad07eec85ad291848885022c..4c5217f1f3911ce3d6af8aec5d80ec1374df534b 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 d9f8878fcd6c68390586e8d42e2ab8d469138d95..13fdc2139bfab807bd61d042433bc13b893c8a84 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 98%
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 3ba14e55a6ada9a29c5e08cbfc570749d456b36e..3edb7a77e71a136d0dcb70185f19f25b0d193eb0 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
@@ -17,8 +17,8 @@ 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.core.{ BiopetCommandLineFunction, BiopetCommandLineFunction$, BiopetJavaCommandLineFunction, SampleLibraryTag }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetJavaCommandLineFunction, SampleLibraryTag }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.{ LastCommitHash, Version }
import org.broadinstitute.gatk.queue.function.{ InProcessFunction, QFunction }
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 97%
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 f75ff65998b4376d3dd651249afdf5557e9ecca1..695b5ca3ae5e6943a4da481714a6bf1c7aa7c855 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 971ceac665c109d46dd4259b6c1c51d907031a9e..ad913a77f4628533798d4e10e360566511ce0f9c 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 97%
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 b9ca3cf915117f49345dd422e63d00de789375fb..503e5a33882b8bfd0aa92186e64a8d99e264367b 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 8be4543c0c57867d999530dbabfa23a7ded44995..144a91f21ae0479438fdb78f9432632d22584318 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 2da59c93bcdec84def20868da789927d2bc8d133..c9b30feeeb796c1b932c7aa61d4ccbd8a2c41837 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 b1fd57e68a88d2906fad1ad977dc9a5ae00e318e..5f3513fd7c22f0b81db0c739f6bb9b70237dc8d7 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 96653b914a88b7d11d3a27800b8809fd82e6da1a..ea7c37b5aef79dc59c942db3ae9127e90e853396 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 4a6740f560bacf980847964d7167823b2dbd0b88..ff19efe11676d2ca66adc172790080f9a9823783 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 086a0059ae0f1c57d4d409103549408dbb2cb2c3..ada8007283b76122005cc5d4e6a0a39c161ea1aa 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 56fc2714448ea23c945b4937eae42f302f1d1621..3c4693b5ead3929b9b1bf7eac95b69c3bed0c83c 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 8fa1594ea396e5b7feaab6c6a04d53e1d5bc7122..bcb5b492168a42b0f7960e80fedc7ee1fbab40c5 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 906a78084d1656054cda33e76eb596256b51d3c8..2aca96da6ebe993381766f50fc699c1c04233b0d 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 84bb3daef4e45e8cacbd4afad7c1539f1f8b48cd..7ec9598e98326dd1477a9d079bf4fe09b31e75af 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 18d8317eb9f7ce2a0d34383cba3c277b5e7ea474..6756f736623693564c344ca11da4a864d1c27977 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 f720d62eb489f859df37905e6d40f07adac9f894..514c9394e8e6d8e663402cc03267fa70c6a2dc73 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 c94fd0c5dcf54bef1b6085604915b09ece1947c3..04a61ae0f9af329ac49252f93ccad829c60b7088 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 94cd83a1911de39405fc50864cc4aae368eedf8e..5e90a5a625c992436a340a874bf60015c19b44ab 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 b6cb49aa695a4180197a347a89b7545596b91c13..02678aac229d0113b19b8e2d3dfbb4eca53793ad 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 461d58b60666f1a85cf1477acd833a1b906cc0dd..39a4fd184fdb73ea853e0b4a0419151773a377dc 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 9e2a7d19c9935fc7958e57fef10f8225170fbeca..b686e80225de8203af40b765764a0c1021e4446d 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 87e14cccd0eae9b64fcf0f0c75375676ef0c2c8d..0b85cb934da432a171b68b4a9a2242774a98537f 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 40889416b9f1ea5ce33fc7e91c69cbe12edd567b..d69faa092303665a1c493686f3a1752010a9ef2a 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 0bcb3c3406aed5886dac522c8bab7db1ac0d1a9b..0379c36d9ace680b7833bf226912504bb619f8e2 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/pipelines/MultisamplePipelineTemplate.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
deleted file mode 100644
index 1d6390b257b27e896966734fdcbe1335a0026642..0000000000000000000000000000000000000000
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
+++ /dev/null
@@ -1,81 +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.pipelines
-
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
-import org.broadinstitute.gatk.queue.QScript
-
-/** Template for a multisample pipeline */
-class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript {
- def this() = this(null)
-
- /** Location of summary file */
- def summaryFile: File = new File(outputDir, "MultisamplePipelineTemplate.summary.json")
-
- /** File to add to the summary */
- def summaryFiles: Map[String, File] = Map()
-
- /** Pipeline settings to add to the summary */
- def summarySettings: Map[String, Any] = Map()
-
- /** Function to make a sample */
- def makeSample(id: String) = new Sample(id)
-
- /** This class will contain jobs and libraries for a sample */
- class Sample(sampleId: String) extends AbstractSample(sampleId) {
- /** Sample specific files for summary */
- def summaryFiles: Map[String, File] = Map()
-
- /** Sample specific stats for summary */
- def summaryStats: Map[String, Any] = Map()
-
- /** Function to make a library */
- def makeLibrary(id: String) = new Library(id)
-
- /** This class will contain all jobs for a library */
- class Library(libId: String) extends AbstractLibrary(libId) {
- /** Library specific files for summary */
- def summaryFiles: Map[String, File] = Map()
-
- /** Library specific stats for summary */
- def summaryStats: Map[String, Any] = Map()
-
- /** Method to add library jobs */
- protected def addJobs(): Unit = {
- }
- }
-
- /** Method to add sample jobs */
- protected def addJobs(): Unit = {
- }
- }
-
- /** Method where multisample jobs are added */
- def addMultiSampleJobs(): Unit = {
- }
-
- /** This is executed before the script starts */
- def init(): Unit = {
- }
-
- /** Method where jobs must be added */
- def biopetScript() {
- }
-}
-
-/** Object to let to generate a main method */
-object MultisamplePipelineTemplate extends PipelineCommand
\ No newline at end of file
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-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
similarity index 51%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala
rename to public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
index 2bfb9b10584683d798947da42ebd65fbe040ed3c..2ee9d97e17ef35cbf6573bf0fa91bb5fc8f76b2c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
@@ -13,24 +13,26 @@
* 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.pipelines
+package nl.lumc.sasc.biopet.extensions.tools
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import org.broadinstitute.gatk.queue.QScript
+import java.io.File
-/** Template for a pipeline */
-class PipelineTemplate(val root: Configurable) extends QScript with BiopetQScript {
- def this() = this(null)
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
- /** This is executed before the script starts */
- def init() {
- }
+class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
+ def toolObject = nl.lumc.sasc.biopet.tools.SageCountFastq
- /** Method where jobs must be added */
- def biopetScript() {
- }
-}
+ @Input(doc = "Input fasta", shortName = "input", required = true)
+ var input: File = _
+
+ @Output(doc = "Output tag library", shortName = "output", required = true)
+ var output: File = _
-/** Object to let to generate a main method */
-object PipelineTemplate extends PipelineCommand
+ 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 85%
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 8eacd72b9b248b3c7f182eeeacf53b1bd084adf5..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
@@ -17,66 +17,15 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ File, PrintWriter }
-import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
+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
-import scala.collection.parallel.ParMap
-
-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 cmdLine = super.cmdLine +
- 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,
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 71%
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 c1f476f563b202dc236daad195bbe4e7ab88b5a8..f9646c4c9ebe7473e5ccb39e833d8ae87176b84a 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 scala.collection.JavaConversions._
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 cmdLine = super.cmdLine + 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
@@ -80,8 +52,7 @@ object BedToInterval extends ToolCommand {
val writer = new PrintWriter(commandArgs.outputFile)
val inputSam = SamReaderFactory.makeDefault.open(commandArgs.bamFile)
- val refs = for (SQ <- inputSam.getFileHeader.getSequenceDictionary.getSequences.toArray) yield {
- val record = SQ.asInstanceOf[SAMSequenceRecord]
+ val refs = for (record <- inputSam.getFileHeader.getSequenceDictionary.getSequences) yield {
writer.write("@SQ\tSN:" + record.getSequenceName + "\tLN:" + record.getSequenceLength + "\n")
record.getSequenceName -> record.getSequenceLength
}
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 b1804f146332c2d3e6b337e9875ba1c5ae4d591f..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 cmdLine = super.cmdLine +
- 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 88%
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 3d2ba4affc090554b5c47dd65bea9466f7720753..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
@@ -18,48 +18,12 @@ 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 cmdLine = super.cmdLine + 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,
outputFile: Option[File] = None,
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 99%
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 919316c2ba04a3c69005a7fa1a1a5464d3629c3a..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
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 77%
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 3f4c3a4e7d392557c71203e2e143250c807e4a81..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 cmdLine = super.cmdLine +
- required("-I", input) +
- repeat("-o", output)
-}
+import nl.lumc.sasc.biopet.utils.ToolCommand
object FastqSplitter extends ToolCommand {
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 72%
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 1df78d427509d66aef9b7c30eeb5cc31ee6c0e51..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 cmdLine =
- super.cmdLine +
- 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 99%
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 b6666fcf1013fffc9ec08af7aa85b84c0c187de4..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
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.tools
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
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 e35f30cf30227342de6d51dd40be7a4fbe958515..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 cmdLine = super.cmdLine +
- 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 d192159623b34919179e6983e1bc687c2022ce97..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 cmdLine =
- super.cmdLine +
- 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 410b765bdd5616714339da2930ce17ce36e14006..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 cmdLine = {
- (if (inputMpileup == null) {
- val samtoolsMpileup = new SamtoolsMpileup(this)
- samtoolsMpileup.reference = referenceFasta()
- samtoolsMpileup.input = List(inputBam)
- samtoolsMpileup.cmdPipe + " | "
- } else "") +
- super.cmdLine +
- 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 f393c9dbdfce16a1c266e8cf3a7fb959bb48b0e0..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 cmdLine = super.cmdLine +
- 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 75%
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 e1673ff44fbf3bf4d77b80799f0d9fd01446920f..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 cmdLine = super.cmdLine +
- 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
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 82%
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 c26604821b4df85fadde6c284c8c78f4a9456ca6..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 cmdLine = super.cmdLine +
- 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,
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 78%
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 a156c1adb483c6fedfa2eb40de6314d35289ecb8..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 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 cmdLine = super.cmdLine +
- 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
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
similarity index 98%
rename from public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
rename to public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
index 879e489fd2671504b1df2ddbac11feaea27bf6da..ff31439d9f0622ef73e3386e207971caa715a607 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.tools
import java.io.{ PrintWriter, File }
-import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.utils.ConfigUtils._
+import nl.lumc.sasc.biopet.utils.ToolCommand
import scala.collection.mutable
import scala.io.Source
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 80%
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 148fb4341941acc0df32b1efdc1d997428a6af61..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
@@ -18,11 +18,7 @@ package nl.lumc.sasc.biopet.tools
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 cmdLine = super.cmdLine + 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 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._
@@ -114,7 +54,7 @@ object SeqStat extends ToolCommand {
head(
s"""
- |$commandName - Summarize FastQ
+ |$commandName - Summarize FastQ
""".stripMargin)
opt[File]('i', "fastq") required () unbounded () valueName "<fastq>" action { (x, c) =>
@@ -330,3 +270,11 @@ object SeqStat extends ToolCommand {
}
}
}
+
+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 64d8e7c10beda6ba6cb3fec90dbc16c285d7bd5c..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 cmdLine = super.cmdLine +
- 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 97%
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 cab4992805ff336f7bcc74c39c8241e163132a84..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
@@ -16,10 +16,9 @@
package nl.lumc.sasc.biopet.tools
import java.io.{ PrintWriter, File }
-import java.nio.file.Paths
-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
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 92%
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 0ca7ea04255d49bde04f8f09d3dfb51ffe31c1fa..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
@@ -20,40 +20,12 @@ 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 cmdLine = super.cmdLine +
- 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[tools] case class Trio(child: String, father: String, mother: String) {
@@ -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())
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 91%
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 c1b4ca49c0647844d3d5cbd27e483d01b925e71e..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 cmdLine = super.cmdLine +
- 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,
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 85%
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 7a89433949ebd5d042a60cb51c25f7ed130e599f..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
@@ -21,49 +21,10 @@ import java.util
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 nl.lumc.sasc.biopet.utils.ToolCommand
import nl.lumc.sasc.biopet.utils.VcfUtils.scalaListToJavaObjectArrayList
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.collection.JavaConversions._
-import scala.collection.JavaConverters._
-
-/**
- * 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 cmdLine = super.cmdLine +
- 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
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 2518113bac32bf4f1a58a102d16d49bb14ae63f7..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 = 4.0
-
- override def cmdLine = super.cmdLine +
- 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-framework/src/test/resources/chrQ2.vcf b/public/biopet-tools/src/test/resources/chrQ2.vcf
similarity index 100%
rename from public/biopet-framework/src/test/resources/chrQ2.vcf
rename to public/biopet-tools/src/test/resources/chrQ2.vcf
diff --git a/public/biopet-framework/src/test/resources/chrQ2.vcf.gz b/public/biopet-tools/src/test/resources/chrQ2.vcf.gz
similarity index 100%
rename from public/biopet-framework/src/test/resources/chrQ2.vcf.gz
rename to public/biopet-tools/src/test/resources/chrQ2.vcf.gz
diff --git a/public/biopet-framework/src/test/resources/chrQ2.vcf.gz.tbi b/public/biopet-tools/src/test/resources/chrQ2.vcf.gz.tbi
similarity index 100%
rename from public/biopet-framework/src/test/resources/chrQ2.vcf.gz.tbi
rename to public/biopet-tools/src/test/resources/chrQ2.vcf.gz.tbi
diff --git a/public/biopet-framework/src/test/resources/chrQ_allN.fa b/public/biopet-tools/src/test/resources/chrQ_allN.fa
similarity index 100%
rename from public/biopet-framework/src/test/resources/chrQ_allN.fa
rename to public/biopet-tools/src/test/resources/chrQ_allN.fa
diff --git a/public/biopet-framework/src/test/resources/chrQ_allN.fa.fai b/public/biopet-tools/src/test/resources/chrQ_allN.fa.fai
similarity index 100%
rename from public/biopet-framework/src/test/resources/chrQ_allN.fa.fai
rename to public/biopet-tools/src/test/resources/chrQ_allN.fa.fai
diff --git a/public/biopet-framework/src/test/resources/fake_chrQ.dict b/public/biopet-tools/src/test/resources/fake_chrQ.dict
similarity index 100%
rename from public/biopet-framework/src/test/resources/fake_chrQ.dict
rename to public/biopet-tools/src/test/resources/fake_chrQ.dict
diff --git a/public/biopet-framework/src/test/resources/fake_chrQ.fa b/public/biopet-tools/src/test/resources/fake_chrQ.fa
similarity index 100%
rename from public/biopet-framework/src/test/resources/fake_chrQ.fa
rename to public/biopet-tools/src/test/resources/fake_chrQ.fa
diff --git a/public/biopet-framework/src/test/resources/fake_chrQ.fa.fai b/public/biopet-tools/src/test/resources/fake_chrQ.fa.fai
similarity index 100%
rename from public/biopet-framework/src/test/resources/fake_chrQ.fa.fai
rename to public/biopet-tools/src/test/resources/fake_chrQ.fa.fai
diff --git a/public/biopet-framework/src/test/resources/flagstat_crossreport.txt b/public/biopet-tools/src/test/resources/flagstat_crossreport.txt
similarity index 100%
rename from public/biopet-framework/src/test/resources/flagstat_crossreport.txt
rename to public/biopet-tools/src/test/resources/flagstat_crossreport.txt
diff --git a/public/biopet-framework/src/test/resources/flagstat_crosstrue.txt b/public/biopet-tools/src/test/resources/flagstat_crosstrue.txt
similarity index 100%
rename from public/biopet-framework/src/test/resources/flagstat_crosstrue.txt
rename to public/biopet-tools/src/test/resources/flagstat_crosstrue.txt
diff --git a/public/biopet-framework/src/test/resources/flagstat_report.txt b/public/biopet-tools/src/test/resources/flagstat_report.txt
similarity index 100%
rename from public/biopet-framework/src/test/resources/flagstat_report.txt
rename to public/biopet-tools/src/test/resources/flagstat_report.txt
diff --git a/public/biopet-framework/src/test/resources/flagstat_summary.txt b/public/biopet-tools/src/test/resources/flagstat_summary.txt
similarity index 100%
rename from public/biopet-framework/src/test/resources/flagstat_summary.txt
rename to public/biopet-tools/src/test/resources/flagstat_summary.txt
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-framework/src/test/resources/mini.transcriptome.fa b/public/biopet-tools/src/test/resources/mini.transcriptome.fa
similarity index 100%
rename from public/biopet-framework/src/test/resources/mini.transcriptome.fa
rename to public/biopet-tools/src/test/resources/mini.transcriptome.fa
diff --git a/public/biopet-framework/src/test/resources/no_sample.tsv b/public/biopet-tools/src/test/resources/no_sample.tsv
similarity index 100%
rename from public/biopet-framework/src/test/resources/no_sample.tsv
rename to public/biopet-tools/src/test/resources/no_sample.tsv
diff --git a/public/biopet-framework/src/test/resources/number.tsv b/public/biopet-tools/src/test/resources/number.tsv
similarity index 100%
rename from public/biopet-framework/src/test/resources/number.tsv
rename to public/biopet-tools/src/test/resources/number.tsv
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-framework/src/test/resources/paired01.pileup b/public/biopet-tools/src/test/resources/paired01.pileup
similarity index 100%
rename from public/biopet-framework/src/test/resources/paired01.pileup
rename to public/biopet-tools/src/test/resources/paired01.pileup
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-framework/src/test/resources/sageAllGenesTest.tsv b/public/biopet-tools/src/test/resources/sageAllGenesTest.tsv
similarity index 100%
rename from public/biopet-framework/src/test/resources/sageAllGenesTest.tsv
rename to public/biopet-tools/src/test/resources/sageAllGenesTest.tsv
diff --git a/public/biopet-framework/src/test/resources/sageNoAntiTest.tsv b/public/biopet-tools/src/test/resources/sageNoAntiTest.tsv
similarity index 100%
rename from public/biopet-framework/src/test/resources/sageNoAntiTest.tsv
rename to public/biopet-tools/src/test/resources/sageNoAntiTest.tsv
diff --git a/public/biopet-framework/src/test/resources/sageNoTagsTest.tsv b/public/biopet-tools/src/test/resources/sageNoTagsTest.tsv
similarity index 100%
rename from public/biopet-framework/src/test/resources/sageNoTagsTest.tsv
rename to public/biopet-tools/src/test/resources/sageNoTagsTest.tsv
diff --git a/public/biopet-framework/src/test/resources/sageTest.tsv b/public/biopet-tools/src/test/resources/sageTest.tsv
similarity index 100%
rename from public/biopet-framework/src/test/resources/sageTest.tsv
rename to public/biopet-tools/src/test/resources/sageTest.tsv
diff --git a/public/biopet-framework/src/test/resources/same.tsv b/public/biopet-tools/src/test/resources/same.tsv
similarity index 100%
rename from public/biopet-framework/src/test/resources/same.tsv
rename to public/biopet-tools/src/test/resources/same.tsv
diff --git a/public/biopet-framework/src/test/resources/sample.tsv b/public/biopet-tools/src/test/resources/sample.tsv
similarity index 100%
rename from public/biopet-framework/src/test/resources/sample.tsv
rename to public/biopet-tools/src/test/resources/sample.tsv
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-framework/src/test/resources/tagCount.tsv b/public/biopet-tools/src/test/resources/tagCount.tsv
similarity index 100%
rename from public/biopet-framework/src/test/resources/tagCount.tsv
rename to public/biopet-tools/src/test/resources/tagCount.tsv
diff --git a/public/biopet-framework/src/test/resources/test.summary.json b/public/biopet-tools/src/test/resources/test.summary.json
similarity index 100%
rename from public/biopet-framework/src/test/resources/test.summary.json
rename to public/biopet-tools/src/test/resources/test.summary.json
diff --git a/public/biopet-framework/src/test/resources/unvep_online.vcf.gz b/public/biopet-tools/src/test/resources/unvep_online.vcf.gz
similarity index 100%
rename from public/biopet-framework/src/test/resources/unvep_online.vcf.gz
rename to public/biopet-tools/src/test/resources/unvep_online.vcf.gz
diff --git a/public/biopet-framework/src/test/resources/unvep_online.vcf.gz.tbi b/public/biopet-tools/src/test/resources/unvep_online.vcf.gz.tbi
similarity index 100%
rename from public/biopet-framework/src/test/resources/unvep_online.vcf.gz.tbi
rename to public/biopet-tools/src/test/resources/unvep_online.vcf.gz.tbi
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-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
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 100%
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
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-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
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-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
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-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/MpileupToVcfTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/PrefixFastqTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCountFastqTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateLibaryTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCountsTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJsonTest.scala
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 100%
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
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
similarity index 97%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
index 916fd48cc35991c0a6a47be4f646b179d8f66831..6071fceaaed85a943a4f973ac713d24e8b708952 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
+++ b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SummaryToTsvTest.scala
@@ -9,7 +9,7 @@ import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
-import nl.lumc.sasc.biopet.core.summary.Summary
+import nl.lumc.sasc.biopet.utils.summary.Summary
/**
* Created by ahbbollen on 31-8-15.
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
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-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
similarity index 100%
rename from public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
rename to public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
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 100%
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
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 100%
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
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 fb585c678361cada7336cb407a64476990fa981a..5bd686c7e20a6ba37f407f44a0a9c83144aabb8d 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.{ SeqStat, FastqSync }
+import nl.lumc.sasc.biopet.extensions.{ Pbzip2, Zcat, Gzip, Sickle }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
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 b50adb4d7d1c72cba75835bac433f18d52d830fd..bcbc337a043d11acdc7bcb579a6f65dcff2e4074 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
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.{ Cat, Ln }
+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) {
var fastqc: Fastqc = _
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 70565ffdd2e719c5a7b478b4184ed9b468d416f3..2270f6ef8752298662f1b513414e657c529278c0 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 593c0a53cca200f50c2f4bbeec57eb63d7618d3c..497fe21e342ed754e21f6be253b1ae5fdd0813fb 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