From 90a053ea935ea6868008bacc9b6d96cf8dd3644a Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Sat, 5 Nov 2011 22:40:45 -0400 Subject: [PATCH] Don't change the mapping quality of MQ=255 reads in IR --- .../sting/gatk/walkers/indels/IndelRealigner.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 60b1f8a88..ba031c497 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -817,7 +817,8 @@ public class IndelRealigner extends ReadWalker { // For now, we will just arbitrarily add 10 to the mapping quality. [EB, 6/7/2010]. // TODO -- we need a better solution here GATKSAMRecord read = aRead.getRead(); - read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254)); + if ( read.getMappingQuality() != 255 ) // 255 == Unknown, so don't modify it + read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254)); // before we fix the attribute tags we first need to make sure we have enough of the reference sequence int neededBasesToLeft = leftmostIndex - read.getAlignmentStart();