From 9d86b1ed467937070103fe85d169b693965c3128 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 12 Mar 2015 14:12:26 +0100
Subject: [PATCH] Fix BamMetrics to use file in stead of directory Fix
markduplicates to not overwrite bam file with metrics file
---
.../sasc/biopet/pipelines/bammetrics/BamMetrics.scala | 5 +++--
.../scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala | 8 --------
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala | 2 +-
3 files changed, 4 insertions(+), 11 deletions(-)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 86519c398..6d2f519aa 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -88,8 +88,9 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
for (bedFile <- bedFiles) {
//TODO: Add target jobs to summary
- val targetDir = new File(outputDir, bedFile.getName.stripSuffix(".bed"))
- val targetInterval = BedToInterval(this, bedFile, inputBam, targetDir)
+ val targetDir = bedFile.getParentFile
+ val targetFile = new File(outputDir, bedFile.getName.stripSuffix(".bed") + ".interval")
+ val targetInterval = BedToInterval(this, bedFile, inputBam, targetFile)
add(targetInterval, true)
add(CalculateHsMetrics(this, inputBam, if (baitIntervalFile != null) baitIntervalFile
else targetInterval.output, targetInterval.output, targetDir))
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
index 187c8e816..55b13c542 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
@@ -43,14 +43,6 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio
}
object BedToInterval extends ToolCommand {
- def apply(root: Configurable, inputBed: File, inputBam: File, outputDir: String): BedToInterval = {
- val bedToInterval = new BedToInterval(root)
- bedToInterval.input = inputBed
- bedToInterval.bamFile = inputBam
- bedToInterval.output = new File(outputDir, inputBed.getName.stripSuffix(".bed") + ".interval")
- return bedToInterval
- }
-
def apply(root: Configurable, inputBed: File, inputBam: File, output: File): BedToInterval = {
val bedToInterval = new BedToInterval(root)
bedToInterval.input = inputBed
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index f0f2c69af..d98b01157 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -219,7 +219,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
val md = new MarkDuplicates(qscript)
md.input = input
md.output = new File(sampleDir, sampleId + ".dedup.bam")
- md.outputMetrics = new File(sampleDir, sampleId + ".dedup.bam")
+ md.outputMetrics = new File(sampleDir, sampleId + ".dedup.metrics")
md.isIntermediate = isIntermediate
add(md)
addSummarizable(md, "mark_duplicates")
--
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