Commit 34ffaaf0 authored by bow's avatar bow
Browse files

Merge branch 'fix-vcf_filter' into 'develop'

Fixed bug in vcffilter

Fixes #313 

See merge request !370
parents 3cc33596 f5f2787f
......@@ -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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