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Forgot to say that the mate is unmapped too. This is necessary to prevent SAM-JDK from yelling at me about an invalid SAM file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@759 348d0f76-0448-11de-a6fe-93d51630548a
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kiran 2009-05-20 15:38:51 +00:00
parent 96e73e496a
commit 505f588768
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
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@ -180,6 +180,7 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
SAMRecord sr = new SAMRecord(sfh);
sr.setReadName(runBarcode + ":" + rr.getReadKey() + "#0");
sr.setMateUnmappedFlag(true);
sr.setReadUmappedFlag(true);
sr.setReadString(rr.getSequenceAsString());
sr.setBaseQualities(rr.getQuals());