Commit 4c3c746b authored by bow's avatar bow
Browse files

Merge branch 'fix-haplotypercaller' into 'develop'

fixed a config value



See merge request !417
parents baa5ab44 a50e42cc
......@@ -90,7 +90,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
/** Mode for emitting reference confidence scores */
@Argument(fullName = "emitRefConfidence", shortName = "ERC", doc = "Mode for emitting reference confidence scores", required = false, exclusiveOf = "", validation = "")
var emitRefConfidence: String = _
var emitRefConfidence: Option[String] = config("emitRefConfidence")
/** File to which assembled haplotypes should be written */
@Output(fullName = "bamOutput", shortName = "bamout", doc = "File to which assembled haplotypes should be written", required = false, exclusiveOf = "", validation = "")
......@@ -522,12 +522,4 @@ object HaplotypeCaller {
hc.out = outputFile
hc
}
def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
val hc = apply(root, List(inputFile), outputFile)
hc.emitRefConfidence = "GVCF"
hc.variant_index_type = Some("LINEAR")
hc.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
hc
}
}
......@@ -34,9 +34,16 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
def getGvcfs = gVcfFiles
override def fixedValues = Map("haplotypecaller" -> Map("emitRefConfidence" -> "GVCF"))
override def defaults = Map("haplotypecaller" -> Map(
"variant_index_type" -> "LINEAR",
"variant_index_parameter" -> 128000)
)
def biopetScript() {
val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
val hc = gatk.HaplotypeCaller.gvcf(this, inputBam, new File(outputDir, sample + ".gvcf.vcf.gz"))
val hc = gatk.HaplotypeCaller(this, List(inputBam), new File(outputDir, sample + ".gvcf.vcf.gz"))
add(hc)
sample -> hc.out
}
......
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