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Fixed Umapped misspelling 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5196 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-04 22:21:41 +00:00
parent 03f265d8bd
commit 0ad1ea4aa1
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/alignment/Alignment.java
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@ -202,7 +202,7 @@ public class Alignment {
read.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START); read.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
if(alignment != null) { if(alignment != null) {
read.setReadUmappedFlag(false); read.setReadUnmappedFlag(false);
read.setReferenceIndex(alignment.getContigIndex()); read.setReferenceIndex(alignment.getContigIndex());
read.setAlignmentStart((int)alignment.getAlignmentStart()); read.setAlignmentStart((int)alignment.getAlignmentStart());
read.setReadNegativeStrandFlag(alignment.isNegativeStrand()); read.setReadNegativeStrandFlag(alignment.isNegativeStrand());

4
java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
View File

@ -164,7 +164,7 @@ public class ArtificialSAMUtils {
record.setBaseQualities(q); record.setBaseQualities(q);
if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) { if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
record.setReadUmappedFlag(true); record.setReadUnmappedFlag(true);
} }
return record; return record;
} }
@ -189,7 +189,7 @@ public class ArtificialSAMUtils {
rec.setReadBases(bases); rec.setReadBases(bases);
rec.setBaseQualities(qual); rec.setBaseQualities(qual);
if (refIndex == -1) { if (refIndex == -1) {
rec.setReadUmappedFlag(true); rec.setReadUnmappedFlag(true);
} }
return rec; return rec;
} }