Merge branch 'develop' into feature-gentrap

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
	public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
@@ -21,5 +21,5 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
   reference_sequence = config("reference")
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
-  if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
+  if (config.contains("pedigree")) pedigree = config("pedigree")
 }

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala → protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -3,7 +3,7 @@
  * 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.extensions.gatk
+package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable

protected/biopet-gatk-pipelines/pom.xml

@@ -39,5 +39,27 @@
             <artifactId>Mapping</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Basty</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>Shiva</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_2.11</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 </project>

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala

+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.pipelines.basty.BastyTrait
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 3/4/15.
+ */
+class Basty(val root: Configurable) extends QScript with BastyTrait {
+  qscript =>
+  def this() = this(null)
+
+  override def variantcallers = List("unifiedgenotyper")
+
+  override lazy val shiva = new Shiva(qscript)
+}
+
+object Basty extends PipelineCommand
\ No newline at end of file

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

@@ -7,7 +7,7 @@ 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.extensions.gatk.{ GenotypeGVCFs, SelectVariants }
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ SelectVariants, GenotypeGVCFs }
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -10,9 +10,9 @@ import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
 import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineVariants, CombineGVCFs }
 import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import scala.collection.JavaConversions._
-import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, CombineGVCFs }
 import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
 import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics