From 3990eb3f85a4bda86db6bfb9c3b6fa89ec595bfa Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 10 Jun 2014 17:44:39 +0200
Subject: [PATCH] Changed filenames of bam files at star
---
.../java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 0d9497c39..db9681488 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -90,7 +90,7 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
} else if (aligner == "star") {
val starCommand = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.outputDir = qscript.outputDir + "star/"; init}
add(starCommand)
- bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), swapExt(outputDir,starCommand.outputSam,".sam",".bam"), outputDir)
+ bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), new File(outputDir + outputName + ".bam"), outputDir)
} else if (aligner == "star-2pass") {
val starCommand_pass1 = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2;
this.outputDir = qscript.outputDir + "star-2pass/aln-pass1/"; init}
@@ -103,7 +103,7 @@ class Mapping(private var globalConfig: Config) extends QScript with BiopetQScri
val starCommand_pass2 = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.deps ++= starCommand_reindex.outputs;
this.outputDir = qscript.outputDir + "star-2pass/aln-pass2/"; this.genomeDir = starCommand_reindex.outputDir; init}
add(starCommand_pass2)
- bamFile = addAddOrReplaceReadGroups(List(starCommand_pass2.outputSam), swapExt(outputDir,starCommand_pass2.outputSam,".sam",".bam"), outputDir)
+ bamFile = addAddOrReplaceReadGroups(List(starCommand_pass2.outputSam), new File(outputDir + outputName + ".bam"), outputDir)
} else throw new IllegalStateException("Option Alginer: '" + aligner + "' is not valid")
if (!skipMarkduplicates) bamFile = addMarkDuplicates(List(bamFile), swapExt(outputDir,bamFile,".bam",".dedup.bam"), outputDir)
--
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