From 6483fd1fec6b42435a523b9c2854608ad450a520 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Thu, 29 Oct 2015 13:38:11 +0100
Subject: [PATCH] Remove sambamba and use samtools for extracting pairs of
unmapped reads (not the advanced query)
---
.../sasc/biopet/pipelines/gears/Gears.scala | 28 +++++++++++++------
1 file changed, 19 insertions(+), 9 deletions(-)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index 895ad38ad..d25d04f84 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{PipelineCommand, SampleLibraryTag}
import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
-import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, KrakenReportToJson}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
@@ -73,17 +73,27 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
def biopetScript(): Unit = {
val fastqFiles: List[File] = bamFile.map { bamfile =>
- // sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
- val samFilterUnmapped = new SambambaView(this)
- samFilterUnmapped.input = bamfile
- samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment) and [XH] == null")
- samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam")
- samFilterUnmapped.isIntermediate = false
- add(samFilterUnmapped)
+// // sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
+// val samFilterUnmapped = new SambambaView(this)
+// samFilterUnmapped.input = bamfile
+// samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment) and [XH] == null")
+// samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam")
+// samFilterUnmapped.isIntermediate = false
+// add(samFilterUnmapped)
+
+
+ val samtoolsViewSelectUnmapped = new SamtoolsView(this)
+ samtoolsViewSelectUnmapped.input = bamfile
+ samtoolsViewSelectUnmapped.b = true
+ samtoolsViewSelectUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam")
+ samtoolsViewSelectUnmapped.f = List("4")
+ samtoolsViewSelectUnmapped.F = List("8")
+ samtoolsViewSelectUnmapped.isIntermediate = true
+ add(samtoolsViewSelectUnmapped)
// start bam to fastq (only on unaligned reads) also extract the matesam
val samToFastq = new SamToFastq(this)
- samToFastq.input = samFilterUnmapped.output
+ samToFastq.input = samtoolsViewSelectUnmapped.output
samToFastq.fastqR1 = new File(outputDir, s"$outputName.unmapped.R1.fq.gz")
samToFastq.fastqR2 = new File(outputDir, s"$outputName.unmapped.R2.fq.gz")
samToFastq.fastqUnpaired = new File(outputDir, s"$outputName.unmapped.singleton.fq.gz")
--
GitLab