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A convenience shortcut isReadUnmapped() added: thanks to SAM format specification, 'read unmapped' flag is not always required to be set for an unmapped read; this method checks both the flag and the alignment reference index/start (if those are set to '*' the flag is not required according to the spec!) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1506 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-09-02 17:00:39 +00:00
parent 0e6feff8f2
commit 58debd7e56
1 changed files with 14 additions and 0 deletions
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14
java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
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@ -258,4 +258,18 @@ public class AlignmentUtils {
refLine.append('\n');
return refLine.toString();
}
/**
* Due to (unfortunate) multiple ways to indicate that read is unmapped allowed by SAM format
* specification, one may need this convenience shortcut. Checks both 'read unmapped' flag and
* alignment reference index/start.
* @param r
* @return
*/
public static boolean isReadUnmapped(final SAMRecord r) {
if ( r.getReadUnmappedFlag() ) return true;
if ( r.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX ||
r.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ) return true;
return false;
}
}