Commit a50e42cc authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

remove gvf method

parent 95f8441a
...@@ -522,12 +522,4 @@ object HaplotypeCaller { ...@@ -522,12 +522,4 @@ object HaplotypeCaller {
hc.out = outputFile hc.out = outputFile
hc hc
} }
def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
val hc = apply(root, List(inputFile), outputFile)
hc.emitRefConfidence = Some("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 { ...@@ -34,9 +34,16 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
def getGvcfs = gVcfFiles 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() { def biopetScript() {
val gvcfFiles = for ((sample, inputBam) <- inputBams) yield { 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) add(hc)
sample -> hc.out sample -> hc.out
} }
......
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