Merge branch 'develop' into feature-gentrap

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala

@@ -21,7 +21,10 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
-class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
+/**
+ * Extension for Tophat
+ */
+class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "FastQ file(s) R1", shortName = "R1")
   var R1: List[File] = List.empty[File]

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -7,6 +7,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
+ * Extension for VariantEffectPredictor
  * Created by ahbbollen on 15-1-15.
  */
 class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction {
@@ -134,6 +135,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
     }
   }
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required(vep_script) +
     required("-i", input) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala

@@ -27,6 +27,7 @@ class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
   var clip: Boolean = config("clip", default = false)
   var unc: Boolean = config("unc", default = false)
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     optional("-blockSize=", blockSize, spaceSeparated = false) +
     optional("-itemsPerSlot=", itemsPerSlot, spaceSeparated = false) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala

@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 
+/** Extension for zcat */
 class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Zipped file")
   var input: File = _
@@ -29,10 +30,12 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
 
   executable = config("exe", default = "zcat")
 
+  /** Returns command to execute */
   def cmdLine = required(executable) + required(input) + " > " + required(output)
 }
 
 object Zcat {
+  /** Returns a default zcat */
   def apply(root: Configurable, input: File, output: File): Zcat = {
     val zcat = new Zcat(root)
     zcat.input = input

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
+/** General abstract class for bedtools extensions */
 abstract class Bedtools extends BiopetCommandLineFunction {
   override def subPath = "bedtools" :: super.subPath
   executable = config("exe", default = "bedtools", submodule = "bedtools")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 import java.io.File
 
+/** Extension for bedtools coverage */
 class BedtoolsCoverage(val root: Configurable) extends Bedtools {
 
   @Input(doc = "Input file (bed/gff/vcf/bam)")
@@ -45,6 +46,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
     if (input.getName.endsWith(".bam")) inputTag = "-abam"
   }
 
+  /** Returns command to execute */
   def cmdLine = required(executable) + required("coverage") +
     required(inputTag, input) +
     required("-b", intersectFile) +
@@ -55,6 +57,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
 }
 
 object BedtoolsCoverage {
+  /** Returns defaul bedtools coverage */
   def apply(root: Configurable, input: File, intersect: File, output: File,
             depth: Boolean = true, sameStrand: Boolean = false, diffStrand: Boolean = false): BedtoolsCoverage = {
     val bedtoolsCoverage = new BedtoolsCoverage(root)
@@ -64,6 +67,6 @@ object BedtoolsCoverage {
     bedtoolsCoverage.depth = depth
     bedtoolsCoverage.sameStrand = sameStrand
     bedtoolsCoverage.diffStrand = diffStrand
-    return bedtoolsCoverage
+    bedtoolsCoverage
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala

@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 import java.io.File
 
+/** Extension for bedtools intersect */
 class BedtoolsIntersect(val root: Configurable) extends Bedtools {
 
   @Input(doc = "Input file (bed/gff/vcf/bam)")
@@ -42,6 +43,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
     if (input.getName.endsWith(".bam")) inputTag = "-abam"
   }
 
+  /** Returns command to execute */
   def cmdLine = required(executable) + required("intersect") +
     required(inputTag, input) +
     required("-b", intersectFile) +
@@ -51,6 +53,7 @@ class BedtoolsIntersect(val root: Configurable) extends Bedtools {
 }
 
 object BedtoolsIntersect {
+  /** Returns default bedtools intersect */
   def apply(root: Configurable, input: File, intersect: File, output: File,
             minOverlap: Double = 0, count: Boolean = false): BedtoolsIntersect = {
     val bedtoolsIntersect = new BedtoolsIntersect(root)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala

@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.bwa
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 /**
+ * General bwa extension
+ *
  * Created by pjvan_thof on 1/16/15.
  */
 abstract class Bwa extends BiopetCommandLineFunction {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala

@@ -6,6 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
+ * Extension for bwa aln
+ *
+ * Based on version 0.7.12-r1039
+ *
  * Created by pjvan_thof on 1/16/15.
  */
 class BwaAln(val root: Configurable) extends Bwa {
@@ -44,6 +48,7 @@ class BwaAln(val root: Configurable) extends Bwa {
   override val defaultVmem = "5G"
   override val defaultThreads = 8
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required("aln") +
     optional("-n", n) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

@@ -22,6 +22,11 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
+/**
+ * Extension for bwa mem
+ *
+ * Based on version 0.7.12-r1039
+ */
 class BwaMem(val root: Configurable) extends Bwa {
   @Input(doc = "Fastq file R1", shortName = "R1")
   var R1: File = _

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala

@@ -10,7 +10,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
  *
  * based on executable version 0.7.10-r789
  *
- * @param root Configurable
  */
 class BwaSampe(val root: Configurable) extends Bwa {
   @Input(doc = "Fastq file R1", required = true)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala

@@ -6,7 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
- * Created by pjvan_thof on 1/16/15.
+ * BWA samse wrapper
+ *
+ * based on executable version 0.7.10-r789
+ *
  */
 class BwaSamse(val root: Configurable) extends Bwa {
   @Input(doc = "Fastq file", required = true)
@@ -24,6 +27,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
   var n: Option[Int] = config("n")
   var r: String = _
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required("samse") +
     optional("-n", n) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala

@@ -6,6 +6,7 @@ package nl.lumc.sasc.biopet.extensions.igvtools
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
+/** General igvtools extension */
 abstract class IGVTools extends BiopetCommandLineFunction {
   executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
   override def versionCommand = executable + " version"

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

@@ -61,6 +61,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
       throw new IllegalArgumentException("TDF file should have a .tdf file-extension"))
   }
 
+  /** Returns command to execute */
   def cmdLine = {
     required(executable) +
       required("count") +
@@ -81,10 +82,7 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
       required(genomeChromSizes)
   }
 
-  /**
-   * This part should never fail, these values are set within this wrapper
-   *
-   */
+  /** This part should never fail, these values are set within this wrapper */
   private def outputArg: String = {
     (tdf, wig) match {
       case (None, None)       => throw new IllegalArgumentException("Either TDF or WIG should be supplied");

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala

@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.macs2
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 /**
+ * General igvtools extension
+ *
  * Created by sajvanderzeeuw on 12/19/14.
  */
 abstract class Macs2 extends BiopetCommandLineFunction {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala

@@ -5,6 +5,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
+/** Extension for macs2*/
 class Macs2CallPeak(val root: Configurable) extends Macs2 {
   @Input(doc = "Treatment input", required = true)
   var treatment: File = _
@@ -56,6 +57,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
   var broadcutoff: Option[Int] = config("broadcutoff")
   var callsummits: Boolean = config("callsummits", default = false)
 
+  /** Sets output files */
   override def beforeGraph: Unit = {
     if (name.isEmpty) throw new IllegalArgumentException("Name is not defined")
     if (outputdir == null) throw new IllegalArgumentException("Outputdir is not defined")
@@ -67,6 +69,7 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
     output_gapped = new File(outputdir + name.get + ".gappedPeak")
   }
 
+  /** Returns command to execute */
   def cmdLine = {
     required(executable) + required("callpeak") +
       required("--treatment", treatment) + /* Treatment sample */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala

@@ -19,6 +19,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
+/** Extension for picard AddOrReplaceReadGroups */
 class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
   javaMainClass = "picard.sam.AddOrReplaceReadGroups"
 
@@ -61,6 +62,7 @@ class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
   @Argument(doc = "RGPI", required = false)
   var RGPI: Option[Int] = _
 
+  /** Returns command to execute */
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +
@@ -77,6 +79,7 @@ class AddOrReplaceReadGroups(val root: Configurable) extends Picard {
 }
 
 object AddOrReplaceReadGroups {
+  /** Returns default AddOrReplaceReadGroups */
   def apply(root: Configurable, input: File, output: File, sortOrder: String = null): AddOrReplaceReadGroups = {
     val addOrReplaceReadGroups = new AddOrReplaceReadGroups(root)
     addOrReplaceReadGroups.input = input

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala

@@ -19,6 +19,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
+/** Extension for picard CalculateHsMetrics */
 class CalculateHsMetrics(val root: Configurable) extends Picard {
   javaMainClass = "picard.analysis.directed.CalculateHsMetrics"
 
@@ -46,6 +47,7 @@ class CalculateHsMetrics(val root: Configurable) extends Picard {
   @Argument(doc = "BAIT_SET_NAME", required = false)
   var baitSetName: String = _
 
+  /** Returns command to execute */
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +
@@ -58,6 +60,7 @@ class CalculateHsMetrics(val root: Configurable) extends Picard {
 }
 
 object CalculateHsMetrics {
+  /** Returns default CalculateHsMetrics */
   def apply(root: Configurable, input: File, baitIntervals: File, targetIntervals: File, outputDir: File): CalculateHsMetrics = {
     val calculateHsMetrics = new CalculateHsMetrics(root)
     calculateHsMetrics.input = input

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala

@@ -20,6 +20,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
+/** Extension for picard CollectAlignmentSummaryMetrics */
 class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
   javaMainClass = "picard.analysis.CollectAlignmentSummaryMetrics"
 
@@ -50,6 +51,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
   @Argument(doc = "STOP_AFTER", required = false)
   var stopAfter: Option[Long] = config("stopAfter")
 
+  /** Returns command to execute */
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +
@@ -63,6 +65,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
 
   def summaryFiles: Map[String, File] = Map()
 
+  /** Returns stats for summary */
   def summaryStats: Map[String, Any] = Picard.getMetrics(output) match {
     case None => Map()
     case Some((header, content)) =>
@@ -79,6 +82,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
 }
 
 object CollectAlignmentSummaryMetrics {
+  /** Returns default CollectAlignmentSummaryMetrics */
   def apply(root: Configurable, input: File, outputDir: File): CollectAlignmentSummaryMetrics = {
     val collectAlignmentSummaryMetrics = new CollectAlignmentSummaryMetrics(root)
     collectAlignmentSummaryMetrics.input = input

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

@@ -19,6 +19,7 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
+/** Extension for picard CollectGcBiasMetrics */
 class CollectGcBiasMetrics(val root: Configurable) extends Picard {
   javaMainClass = "picard.analysis.CollectGcBiasMetrics"
 
@@ -51,9 +52,9 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
 
   override def beforeGraph {
     if (outputChart == null) outputChart = new File(output + ".pdf")
-    //require(reference.exists)
   }
 
+  /** Returns command to execute */
   override def commandLine = super.commandLine +
     repeat("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +
@@ -67,6 +68,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
 }
 
 object CollectGcBiasMetrics {
+  /** Returns default CollectGcBiasMetrics */
   def apply(root: Configurable, input: File, outputDir: File): CollectGcBiasMetrics = {
     val collectGcBiasMetrics = new CollectGcBiasMetrics(root)
     collectGcBiasMetrics.input :+= input