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Commit c640dc87 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixed reference

parent a39f363c
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CommandLineGATK.scala
View file @ c640dc87
......@@ -324,7 +324,7 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
override def beforeGraph() {
super.beforeGraph()
if (reference_sequence != null) reference_sequence = referenceFasta()
if (reference_sequence == null) reference_sequence = referenceFasta()
input_fileIndexes ++= input_file.filter(orig => orig != null && orig.getName.endsWith(".bam")).flatMap(orig => Array(new File(orig.getPath + ".bai"), new File(orig.getPath.stripSuffix(".bam") + ".bai")))
if (num_threads.isDefined) nCoresRequest = num_threads
if (num_cpu_threads_per_data_thread.isDefined) nCoresRequest = Some(nCoresRequest.getOrElse(1) * num_cpu_threads_per_data_thread.getOrElse(1))
......
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