Commit 33b91781 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed graph issues

parent ef7186db
......@@ -318,7 +318,7 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
override def beforeGraph() {
super.beforeGraph()
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")))
input_fileIndexes ++= input_file.filter(orig => orig != null && orig.getName.endsWith(".bam")).flatMap(orig => Array(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))
}
......
......@@ -156,7 +156,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
/** The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES */
@Input(fullName = "alleles", shortName = "alleles", doc = "The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES", required = false, exclusiveOf = "", validation = "")
var alleles: File = _
var alleles: Option[File] = _
/** Fraction of contamination in sequencing data (for all samples) to aggressively remove */
@Argument(fullName = "contamination_fraction_to_filter", shortName = "contamination", doc = "Fraction of contamination in sequencing data (for all samples) to aggressively remove", required = false, exclusiveOf = "", validation = "")
......@@ -403,15 +403,14 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
if (!org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.isCompressed(out.getPath))
outputFiles :+= VcfUtils.getVcfIndexFile(out)
dbsnp.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
deps ++= comp.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => new File(orig.getPath + ".idx"))
deps ++= comp.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
if (bamOutput != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(bamOutput))
if (!disable_bam_indexing)
outputFiles :+= new File(bamOutput.getPath.stripSuffix(".bam") + ".bai")
if (bamOutput != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(bamOutput))
if (generate_md5)
bamOutputMD5 = new File(bamOutput.getPath + ".md5")
if (alleles != null)
deps :+= new File(alleles.getPath + ".idx")
alleles.foreach(VcfUtils.getVcfIndexFile(_))
num_cpu_threads_per_data_thread = Some(getThreads)
}
......
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