Adding IGVTools for creation of TDF files (Wiggle for IGV)

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

+/**
+ * Created by wyleung on 5-1-15.
+ */
+
+package nl.lumc.sasc.biopet.extensions.igvtools
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+
+abstract class IGVTools extends BiopetCommandLineFunction {
+  executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
+  override def versionCommand = executable + " version"
+  override val versionRegex = """IGV Version: ([\d\.]) .*""".r
+  override val versionExitcode = List(0)
+}
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

+
+package nl.lumc.sasc.biopet.extensions.igvtools
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import java.io.File
+
+class IGVToolsCount(val root: Configurable) extends IGVTools {
+  @Input(doc = "Bam File")
+  var input: File = _
+
+  @Argument(doc = "Genome name")
+  var genomename: String = _
+
+  @Output(doc = "output File")
+  var output: File = _
+
+  def cmdLine = required(executable) + required("count") + required(input) + required(output) + required(genomename)
+}
+
+object IGVToolsCount {
+  def apply(root: Configurable, input: File, output: File, genomename: String): IGVToolsCount = {
+    val counting = new IGVToolsCount(root)
+    counting.input = input
+    counting.output = output
+    counting.genomename = genomename
+    return counting
+  }
+
+  def apply(root: Configurable, input: File, genomename: String): IGVToolsCount = {
+    return apply(root, input, new File(swapExtension(input.getCanonicalPath)), genomename)
+  }
+
+  private def swapExtension(inputFile: String) = inputFile + ".tdf"
+}
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public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala

@@ -24,6 +24,7 @@ import nl.lumc.sasc.biopet.core.MultiSampleQScript
 import nl.lumc.sasc.biopet.core.PipelineCommand
 
 import nl.lumc.sasc.biopet.extensions.Ln
+import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
 import nl.lumc.sasc.biopet.extensions.sambamba.{ SambambaIndex, SambambaMerge, SambambaMarkdup }
 import nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
 import nl.lumc.sasc.biopet.extensions.svcallers.{ Breakdancer, Delly, CleverCaller }
@@ -91,21 +92,25 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
     val bamFile: File =
       if (libraryBamfiles.size == 1) {
         // When the sample has only 1 run, make a link in the main alignment directory
-        val alignmentlink = Ln(root, libraryBamfiles.head,
+        val alignmentlink = Ln(this, libraryBamfiles.head,
           alignmentDir + sampleID + ".merged.bam", true)
         add(alignmentlink, isIntermediate = true)
         alignmentlink.out
       } else if (libraryBamfiles.size > 1) {
-        val mergeSamFiles = new SambambaMerge(root)
+        val mergeSamFiles = new SambambaMerge(this)
         mergeSamFiles.input = libraryBamfiles
         mergeSamFiles.output = alignmentDir + sampleID + ".merged.bam"
         add(mergeSamFiles, isIntermediate = true)
         mergeSamFiles.output
       } else null
 
-    val bamMarkDup = SambambaMarkdup(root, bamFile)
+    val bamMarkDup = SambambaMarkdup(this, bamFile)
     add(bamMarkDup)
 
+    // create an IGV TDF file
+    val tdfCount = IGVToolsCount(this, bamMarkDup.output, config("genomename", default = "hg19"))
+    add(tdfCount)
+
     /// bamfile will be used as input for the SV callers. First run Clever
     //    val cleverVCF : File = sampleDir + "/" + sampleID + ".clever.vcf"