Commit d66701ba authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed bug in vcffilter

(cherry picked from commit f5f2787f)
parent 6035d15b
......@@ -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
}
/**
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment