From ef5ea6ce339326e0bb196eccfd7eecc7e0d139fd Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 29 Oct 2015 14:07:00 +0100
Subject: [PATCH] Added bammetrics when start from bam file
---
.../lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala | 10 ++++++++++
1 file changed, 10 insertions(+)
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 2b13c8d41..19c11ca88 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
@@ -197,6 +197,16 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
val bamLn = Ln(qscript, oldBamFile, bamFile.get)
bamLn.deps :+= baiLn.output
add(bamLn)
+
+ val bamMetrics = new BamMetrics(qscript)
+ bamMetrics.sampleId = Some(sampleId)
+ bamMetrics.libId = Some(libId)
+ bamMetrics.inputBam = bamFile.get
+ bamMetrics.outputDir = new File(libDir, "metrics")
+ bamMetrics.init()
+ bamMetrics.biopetScript()
+ addAll(bamMetrics.functions)
+ addSummaryQScript(bamMetrics)
}
}
}
--
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