From cfdfd0b924843fbfefdfb0e3e9e5387addaaccf2 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 8 Oct 2015 16:37:12 +0200
Subject: [PATCH] added bam metrics for filtered file
---
.../scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala | 9 +++++++++
1 file changed, 9 insertions(+)
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 fb9004103..fc89aada7 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
@@ -124,11 +124,20 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"), sampleId = Some(sampleId))
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
+
+ val bamMetricsFilter = BamMetrics(qscript, bamFileFilter, new File(sampleDir, "metrics-filter"), sampleId = Some(sampleId))
+ addAll(bamMetricsFilter.functions)
+ bamMetricsFilter.summaryName = "bamMetrics-filter"
+ addSummaryQScript(bamMetricsFilter)
+
addAll(Bam2Wig(qscript, bamFile).functions)
+ addAll(Bam2Wig(qscript, bamFileFilter).functions)
val samtoolsView = new SamtoolsView(qscript)
samtoolsView.input = bamFile
samtoolsView.output = bamFileFilter
+ samtoolsView.b = true
+ samtoolsView.h = true
add(samtoolsView)
val buildBamIndex = new BuildBamIndex(qscript)
--
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