Commit babcd139 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added igvtools

parent d3b973b0
......@@ -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)
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment