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Commit 917ed16d authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix on bamADfilter

parent 4355447e
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
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...@@ -111,7 +111,7 @@ object VcfFilter extends ToolCommand { ...@@ -111,7 +111,7 @@ object VcfFilter extends ToolCommand {
if (record.getAttributeAsInt("DP", -1) >= commandArgs.minTotalDepth && if (record.getAttributeAsInt("DP", -1) >= commandArgs.minTotalDepth &&
genotypes.count(_ == true) >= commandArgs.minSamplesPass && genotypes.count(_ == true) >= commandArgs.minSamplesPass &&
bamADvalues.count(_ == true) >= commandArgs.minSamplesPass) (commandArgs.minBamAlternateDepth <= 0 || bamADvalues.count(_ == true) >= commandArgs.minSamplesPass))
writer.add(record) writer.add(record)
} }
reader.close reader.close
......
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