From 29f7b1e6d6bceacbf848e0754c3e90bb017491b9 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 8 Sep 2010 14:02:38 +0000 Subject: [PATCH] Trivial update git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4229 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 4b38d76eb..4bd2f408f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -589,12 +589,12 @@ public class IndelRealigner extends ReadWalker { // fix the attribute tags if ( read.getAttribute(SAMTag.NM.name()) != null ) - read.setAttribute("NM", SequenceUtil.calculateSamNmTag(read, reference, (int)leftmostIndex-1)); + read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, reference, (int)leftmostIndex-1)); if ( read.getAttribute(SAMTag.UQ.name()) != null ) - read.setAttribute("UQ", SequenceUtil.sumQualitiesOfMismatches(read, reference, (int)leftmostIndex-1)); + read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, reference, (int)leftmostIndex-1)); // TODO -- this is only temporary until Tim adds code to recalculate this value if ( read.getAttribute(SAMTag.MD.name()) != null ) - read.setAttribute("MD", null); + read.setAttribute(SAMTag.MD.name(), null); } } }