Added igvtools

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.bamtobigwig
 import nl.lumc.sasc.biopet.core.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
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
@@ -22,16 +23,19 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
   }
 
   def biopetScript(): Unit = {
-    //TODO: bam -> wig
-
     val bs = new BamToChromSizes(this)
     bs.bamFile = bamFile
     bs.chromSizesFile = bamFile.getAbsoluteFile + ".chromsizes"
     bs.isIntermediate = true
     add(bs)
 
+    val igvCount = new IGVToolsCount(this)
+    igvCount.input = bamFile
+    igvCount.genomeChromSizes = bs.chromSizesFile
+    igvCount.wig = Some(swapExt(outputDir, bamFile, ".bam", ".wig"))
+
     val wigToBigWig = new WigToBigWig(this)
-    //TODO: wigToBigWig.inputWigFile
+    wigToBigWig.inputWigFile = igvCount.wig.get
     wigToBigWig.inputChromSizesFile = bs.chromSizesFile
     wigToBigWig.outputBigWig = bigWigFile
     add(wigToBigWig)