Commit 439da30a authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fix on missing AD field

parent 50b908db
......@@ -268,7 +268,7 @@ object BastyGenerateFasta extends ToolCommand {
val genotype = vcfRecord.getGenotype(cmdArgs.sampleName)
if (genotype == null) return fillAllele("", maxSize)
val AD = genotype.getAD
val AD = if (genotype.hasAD) genotype.getAD else Array.fill(vcfRecord.getAlleles.size())(cmdArgs.minAD)
if (AD == null) return fillAllele("", maxSize)
val maxADid = AD.zipWithIndex.maxBy(_._1)._2
if (AD(maxADid) < cmdArgs.minAD) return fillAllele("", maxSize)
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