From 6cf413e630b4e8d6e69299348fb40c7f45bcdbfa Mon Sep 17 00:00:00 2001 From: asivache Date: Mon, 25 Jan 2010 19:23:44 +0000 Subject: [PATCH] Bug: ExpandedSAMRecord did not treat hard-clipped bases ('H') correctly. Fixed. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2680 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelGenotyperV2Walker.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java index cae8a36dd..bc1c874e1 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java @@ -1105,13 +1105,13 @@ public class IndelGenotyperV2Walker extends ReadWalker { int eventPosition = posOnRef; switch(ce.getOperator()) { + case H: break; // hard clipped reads do not have clipped bases in their sequence, so we just ignore the H element... case I: type = IndelVariant.Type.I; bases = readBases.substring(posOnRead,posOnRead+ce.getLength()); // will increment position on the read below, there's no 'break' statement yet... - case H: case S: - // here we also skip hard and soft-clipped bases on the read; according to SAM format specification, + // here we also skip soft-clipped bases on the read; according to SAM format specification, // alignment start position on the reference points to where the actually aligned // (not clipped) bases go, so we do not need to increment reference position here posOnRead += ce.getLength();