Commit 7734a3c0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added stand_call_conf and stand_emit_conf option

parent 9a25fc2b
...@@ -57,7 +57,7 @@ class GatkGenotyping(val root:Configurable) extends QScript with BiopetQScript { ...@@ -57,7 +57,7 @@ class GatkGenotyping(val root:Configurable) extends QScript with BiopetQScript {
if (configContains("dbsnp")) this.dbsnp = config("dbsnp") if (configContains("dbsnp")) this.dbsnp = config("dbsnp")
if (configContains("scattercount", "genotypegvcfs")) this.scatterCount = config("scattercount", 1, "genotypegvcfs") if (configContains("scattercount", "genotypegvcfs")) this.scatterCount = config("scattercount", 1, "genotypegvcfs")
this.out = outputFile this.out = outputFile
if (config("inputtype", "dna") == "rna") { if (config("inputtype", "dna").getString == "rna") {
this.stand_call_conf = config("stand_call_conf", 20, "haplotypecaller") this.stand_call_conf = config("stand_call_conf", 20, "haplotypecaller")
this.stand_emit_conf = config("stand_emit_conf", 20, "haplotypecaller") this.stand_emit_conf = config("stand_emit_conf", 20, "haplotypecaller")
} else { } else {
......
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