From 0929d42524254b1b6a5b03a5e650c30dc92857c6 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 30 Nov 2015 09:41:02 +0100
Subject: [PATCH] Added bam index file as output file
---
.../sasc/biopet/extensions/gatk/broad/IndelRealigner.scala | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
index 44a3eac66..32cf797a0 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
@@ -8,8 +8,12 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Output
class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
+ @Output
+ protected var bamIndex: File = _
+
if (config.contains("scattercount")) scatterCount = config("scattercount")
}
@@ -19,6 +23,7 @@ object IndelRealigner {
ir.input_file :+= input
ir.targetIntervals = targetIntervals
ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
+ ir.bamIndex = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bai")
ir
}
}
\ No newline at end of file
--
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