From 9497e9492cb6904fac16349ae5cdaadb8a4350d8 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 14 Dec 2011 11:21:28 -0500 Subject: [PATCH] Bug fix for complex records: do not ever reverse clip out a complete allele. --- .../sting/utils/codecs/vcf/AbstractVCFCodec.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index b902f220f..e44c10f1f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -595,6 +595,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec { if ( a.isSymbolic() ) continue; + // we need to ensure that we don't reverse clip out all of the bases from an allele because we then will have the wrong + // position set for the VariantContext (although it's okay to forward clip it all out, because the position will be fine). + if ( a.length() - clipping == 0 ) + return clipping - 1; + if ( a.length() - clipping <= forwardClipping || a.length() - forwardClipping == 0 ) stillClipping = false; else if ( ref.length() == clipping )