From 77e40ed5e5dc6197812f4c4032135b4c4e94b3fb Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sun, 8 Mar 2015 12:37:47 +0100
Subject: [PATCH] Use MergeSamFiles for all merges
---
.../sasc/biopet/pipelines/gentrap/Gentrap.scala | 15 +++++----------
1 file changed, 5 insertions(+), 10 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index b095dc78e..a635d4dc4 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.core.config._
import nl.lumc.sasc.biopet.core.summary._
import nl.lumc.sasc.biopet.extensions.{ HtseqCount, Ln }
-import nl.lumc.sasc.biopet.extensions.picard.{ CollectRnaSeqMetrics, GatherBamFiles, MergeSamFiles, SortSam }
+import nl.lumc.sasc.biopet.extensions.picard.{ CollectRnaSeqMetrics, SortSam, MergeSamFiles }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import nl.lumc.sasc.biopet.pipelines.gentrap.extensions.{ CustomVarScan, Pdflatex, RawBaseCounter }
@@ -511,7 +511,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
case Some(r2j) => List(f1Job.output, r2j.output)
case None => List(f1Job.output)
}
- val combineJob = makeCombineJob(perStrandFiles, createFile(".plus_strand.bam"), gather = true)
+ val combineJob = makeCombineJob(perStrandFiles, createFile(".plus_strand.bam"))
Option(StrandSeparationJobSet(f1Job, r2Job, combineJob))
@@ -552,7 +552,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
case Some(r1j) => List(f2Job.output, r1j.output)
case None => List(f2Job.output)
}
- val combineJob = makeCombineJob(perStrandFiles, createFile(".minus_strand.bam"), gather = true)
+ val combineJob = makeCombineJob(perStrandFiles, createFile(".minus_strand.bam"))
Option(StrandSeparationJobSet(f2Job, r1Job, combineJob))
@@ -648,11 +648,11 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
job
}
- /** Super type of Ln and MergeSamFile */
+ /** Super type of Ln and MergeSamFiles */
private type CombineFileFunction = QFunction { def output: File }
/** Ln or MergeSamFile job, depending on how many inputs are supplied */
- private def makeCombineJob(inFiles: List[File], outFile: File, gather: Boolean = false,
+ private def makeCombineJob(inFiles: List[File], outFile: File,
mergeSortOrder: String = "coordinate"): CombineFileFunction = {
require(inFiles.nonEmpty, "At least one input files for combine job")
if (inFiles.size == 1) {
@@ -660,11 +660,6 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
job.input = inFiles.head
job.output = outFile
job
- } else if (gather) {
- val job = new GatherBamFiles(qscript)
- job.input = inFiles
- job.output = outFile
- job
} else {
val job = new MergeSamFiles(qscript)
job.input = inFiles
--
GitLab