Commit 2c17add4 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed small issues

parent 2b479c4c
......@@ -37,6 +37,13 @@ class SambambaMerge(val parent: Configurable) extends Sambamba {
override def defaultThreads = 4
override def defaultCoreMemory = 4.0
@Output
private var indexOutput: File = _
override def beforeGraph(): Unit = {
indexOutput = new File(output + ".bai")
}
/** Returns command to execute */
def cmdLine: String = required(executable) +
required("merge") +
......
......@@ -267,9 +267,11 @@ trait MultisampleMappingTrait extends MultiSampleQScript
val merge = new SambambaMerge(qscript)
merge.input = libraries.flatMap(_._2.preProcessBam).toList
merge.output = mergedBam
merge.isIntermediate = true
add(merge)
}
add(SambambaMarkdup(qscript, mergedBam, bamFile.get, isIntermediate = !keepMergedFiles))
Ln(qscript, bamFile.get + ".bai", bamFile.get.getAbsolutePath.stripSuffix(".bam") + ".bai")
case _ => throw new IllegalStateException("This should not be possible, unimplemented MergeStrategy?")
}
......
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