Added scala docs for picard

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

@@ -77,7 +77,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       }
       List(bamFile)
     } else {
-      val markDup = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
+      val markDup = MarkDuplicates(this, files, new File(outputDir, outputName + ".dedup.bam"))
       markDup.isIntermediate = useIndelRealigner
       add(markDup)
       if (useIndelRealigner) {

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] = {
     val (header, content) = Picard.getMetrics(output)
 
@@ -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

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

@@ -22,6 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 import scala.collection.immutable.Nil
 
+/** Extension for picard CollectInsertSizeMetrics */
 class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable {
   javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
 
@@ -57,10 +58,9 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
 
   override def beforeGraph {
     outputHistogram = new File(output + ".pdf")
-    //if (outputHistogram == null) outputHistogram = new File(output + ".pdf")
-    //require(reference.exists)
   }
 
+  /** Returns command to execute */
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +
@@ -72,8 +72,10 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
     optional("HISTOGRAM_WIDTH=", histogramWidth, spaceSeparated = false) +
     conditional(assumeSorted, "ASSUME_SORTED=TRUE")
 
+  /** Returns files for summary */
   def summaryFiles: Map[String, File] = Map("output_histogram" -> outputHistogram)
 
+  /** Returns stats for summary */
   def summaryStats: Map[String, Any] = {
     val (header, content) = Picard.getMetrics(output)
     (for (i <- 0 to header.size if i < content.head.size)
@@ -82,6 +84,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
 }
 
 object CollectInsertSizeMetrics {
+  /** Returns default CollectInsertSizeMetrics */
   def apply(root: Configurable, input: File, outputDir: File): CollectInsertSizeMetrics = {
     val collectInsertSizeMetrics = new CollectInsertSizeMetrics(root)
     collectInsertSizeMetrics.input = input

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.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 MarkDuplicates */
 class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
   javaMainClass = "picard.sam.MarkDuplicates"
 
@@ -76,6 +77,7 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
     if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
   }
 
+  /** Returns command to execute */
   override def commandLine = super.commandLine +
     repeat("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +
@@ -93,8 +95,10 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
     optional("READ_NAME_REGEX=", readNameRegex, spaceSeparated = false) +
     optional("OPTICAL_DUPLICATE_PIXEL_DISTANCE=", opticalDuplicatePixelDistance, spaceSeparated = false)
 
+  /** Returns files for summary */
   def summaryFiles: Map[String, File] = Map()
 
+  /** Returns stats for summary */
   def summaryStats: Map[String, Any] = {
     val (header, content) = Picard.getMetrics(outputMetrics)
 
@@ -110,19 +114,12 @@ class MarkDuplicates(val root: Configurable) extends Picard with Summarizable {
   }
 }
 object MarkDuplicates {
-  def apply(root: Configurable, input: List[File], outputDir: String): MarkDuplicates = {
-    val markDuplicates = new MarkDuplicates(root)
-    markDuplicates.input = input
-    markDuplicates.output = new File(outputDir, input.head.getName.stripSuffix(".bam") + ".dedup.bam")
-    markDuplicates.outputMetrics = new File(outputDir, input.head.getName.stripSuffix(".bam") + ".dedup.metrics")
-    return markDuplicates
-  }
-
+  /** Returns default MarkDuplicates */
   def apply(root: Configurable, input: List[File], output: File): MarkDuplicates = {
     val markDuplicates = new MarkDuplicates(root)
     markDuplicates.input = input
     markDuplicates.output = output
     markDuplicates.outputMetrics = new File(output.getParent, output.getName.stripSuffix(".bam") + ".metrics")
-    return markDuplicates
+    markDuplicates
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.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 MergeSamFiles */
 class MergeSamFiles(val root: Configurable) extends Picard {
   javaMainClass = "picard.sam.MergeSamFiles"
 
@@ -43,6 +44,7 @@ class MergeSamFiles(val root: Configurable) extends Picard {
   @Argument(doc = "COMMENT", required = false)
   var comment: Option[String] = config("comment")
 
+  /** Returns command to execute */
   override def commandLine = super.commandLine +
     repeat("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +
@@ -53,12 +55,13 @@ class MergeSamFiles(val root: Configurable) extends Picard {
 }
 
 object MergeSamFiles {
+  /** Returns default MergeSamFiles */
   def apply(root: Configurable, input: List[File], outputDir: File, sortOrder: String = null): MergeSamFiles = {
     val mergeSamFiles = new MergeSamFiles(root)
     mergeSamFiles.input = input
     mergeSamFiles.output = new File(outputDir, input.head.getName.stripSuffix(".bam").stripSuffix(".sam") + ".merge.bam")
     if (sortOrder == null) mergeSamFiles.sortOrder = "coordinate"
     else mergeSamFiles.sortOrder = sortOrder
-    return mergeSamFiles
+    mergeSamFiles
   }
 }
\ No newline at end of file

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

@@ -22,6 +22,11 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument }
 
 import scala.io.Source
 
+/**
+ * General picard extension
+ *
+ * This is based on using class files directly from the jar
+ */
 abstract class Picard extends BiopetJavaCommandLineFunction {
   override def subPath = "picard" :: super.subPath
 
@@ -66,6 +71,11 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
 }
 
 object Picard {
+  /**
+   * This function parse a metrics file in separated values
+   * @param file input metrics file
+   * @return (header, content)
+   */
   def getMetrics(file: File) = {
     val lines = Source.fromFile(file).getLines().toArray
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.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 SamToFastq */
 class SamToFastq(val root: Configurable) extends Picard {
   javaMainClass = "picard.sam.SamToFastq"
 
@@ -70,6 +71,7 @@ class SamToFastq(val root: Configurable) extends Picard {
   @Argument(doc = "includeNonPrimaryAlignments", required = false)
   var includeNonPrimaryAlignments: Boolean = config("includeNonPrimaryAlignments", default = false)
 
+  /** Returns command to execute */
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +
     required("FASTQ=", fastqR1, spaceSeparated = false) +
@@ -90,11 +92,12 @@ class SamToFastq(val root: Configurable) extends Picard {
 }
 
 object SamToFastq {
+  /** Returns default SamToFastq */
   def apply(root: Configurable, input: File, fastqR1: File, fastqR2: File = null): SamToFastq = {
     val samToFastq = new SamToFastq(root)
     samToFastq.input = input
     samToFastq.fastqR1 = fastqR1
     samToFastq.fastqR2 = fastqR2
-    return samToFastq
+    samToFastq
   }
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.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 SortSam */
 class SortSam(val root: Configurable) extends Picard {
   javaMainClass = "picard.sam.SortSam"
 
@@ -39,6 +40,7 @@ class SortSam(val root: Configurable) extends Picard {
     if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
   }
 
+  /** Returns command to execute */
   override def commandLine = super.commandLine +
     required("INPUT=", input, spaceSeparated = false) +
     required("OUTPUT=", output, spaceSeparated = false) +
@@ -46,6 +48,7 @@ class SortSam(val root: Configurable) extends Picard {
 }
 
 object SortSam {
+  /** Returns default SortSam */
   def apply(root: Configurable, input: File, output: File, sortOrder: String = null): SortSam = {
     val sortSam = new SortSam(root)
     sortSam.input = input