From babcd13938977b5553ad5c30127d5d9ca48472c2 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Feb 2015 14:03:03 +0100
Subject: [PATCH] Added igvtools
---
.../sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
index 6618ecfcb..b91aaafae 100644
--- a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+++ b/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)
--
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