From 439da30aedf8de83417783f33c642cd56bb8aeec Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 4 Mar 2015 15:32:13 +0100
Subject: [PATCH] fix on missing AD field
---
.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index ead615fe3..188e8f824 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -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)
--
GitLab