Commit f5f2787f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed bug in vcffilter

parent 3cc33596
......@@ -276,8 +276,10 @@ object VcfFilter extends ToolCommand {
* @return
*/
def minGenomeQuality(record: VariantContext, minGQ: Int, minSamplesPass: Int = 1): Boolean = {
record.getGenotypes.count(x => if (!x.hasGQ) false
else if (x.getGQ >= minGQ) true else false) >= minSamplesPass
record.getGenotypes.count(x =>
if (minGQ == 0) true
else if (!x.hasGQ) false
else if (x.getGQ >= minGQ) true else false) >= minSamplesPass
}
/**
......
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