From 0ad1ea4aa1ed4f4c81b9a4b3817d05c2dcf0ba6d Mon Sep 17 00:00:00 2001 From: depristo Date: Fri, 4 Feb 2011 22:21:41 +0000 Subject: [PATCH] Fixed Umapped misspelling git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5196 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/alignment/Alignment.java | 2 +- .../broadinstitute/sting/utils/sam/ArtificialSAMUtils.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/alignment/Alignment.java b/java/src/org/broadinstitute/sting/alignment/Alignment.java index b296aa56a..ebbc8c1b8 100644 --- a/java/src/org/broadinstitute/sting/alignment/Alignment.java +++ b/java/src/org/broadinstitute/sting/alignment/Alignment.java @@ -202,7 +202,7 @@ public class Alignment { read.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START); if(alignment != null) { - read.setReadUmappedFlag(false); + read.setReadUnmappedFlag(false); read.setReferenceIndex(alignment.getContigIndex()); read.setAlignmentStart((int)alignment.getAlignmentStart()); read.setReadNegativeStrandFlag(alignment.isNegativeStrand()); diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java index 095fe3ab3..2dcdd5ce6 100755 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java @@ -164,7 +164,7 @@ public class ArtificialSAMUtils { record.setBaseQualities(q); if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) { - record.setReadUmappedFlag(true); + record.setReadUnmappedFlag(true); } return record; } @@ -189,7 +189,7 @@ public class ArtificialSAMUtils { rec.setReadBases(bases); rec.setBaseQualities(qual); if (refIndex == -1) { - rec.setReadUmappedFlag(true); + rec.setReadUnmappedFlag(true); } return rec; }