From 2d950663960b51d2796d3a9544e33ac45b7423a2 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 17 Sep 2015 19:28:47 +0200
Subject: [PATCH] Fix sample bamMetrics
---
.../lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala | 7 ++++++-
.../scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala | 2 +-
2 files changed, 7 insertions(+), 2 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 24b0a29b1..defb8361c 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
@@ -186,8 +186,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
object BamMetrics extends PipelineCommand {
/** Make default implementation of BamMetrics and runs script already */
- def apply(root: Configurable, bamFile: File, outputDir: File): BamMetrics = {
+ def apply(root: Configurable,
+ bamFile: File, outputDir: File,
+ sampleId: Option[String] = None,
+ libId: Option[String] = None): BamMetrics = {
val bamMetrics = new BamMetrics(root)
+ bamMetrics.sampleId = sampleId
+ bamMetrics.libId = libId
bamMetrics.inputBam = bamFile
bamMetrics.outputDir = outputDir
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index fcb9aa3e6..195718d5d 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -107,7 +107,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
add(merge)
}
- val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"))
+ val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"), sampleId = Some(sampleId))
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
addAll(Bam2Wig(qscript, bamFile).functions)
--
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