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Changed to use AlignmentUtils.isReadUnmapped() for better consistency with SAM spec; also, it is now explicitly enforced that unmapped reads have <NO_...> values set for ref contig and start upon "remapping" 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1519 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-09-03 16:45:07 +00:00
parent 61d4dd4d01
commit 499b3536a4
1 changed files with 10 additions and 5 deletions
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15
java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
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@ -24,10 +24,7 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.StingException;
public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeLoc> > >{ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeLoc> > >{
@ -204,7 +201,15 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
* @return same read instance that was passed to this method, remapped * @return same read instance that was passed to this method, remapped
*/ */
public SAMRecord remapToMasterReference(SAMRecord r, SAMFileHeader h, boolean discardCrossContig) { public SAMRecord remapToMasterReference(SAMRecord r, SAMFileHeader h, boolean discardCrossContig) {
if ( r.getReadUnmappedFlag() ) return r; // nothing to do if read is unmapped if ( AlignmentUtils.isReadUnmapped(r) ) {
// set to NO_... just in case: in principle, SAM format spec allows unmapped reads (with 'unmapped'
// flag raised) to have reference contig and start position set to arbitrary values for sorting
// purposes; after remapping, these values would make no sense or even cause a crash when reading
// remapped bam
r.setReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
r.setAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
return r; // nothing to do if read is unmapped
}
int customStart = r.getAlignmentStart(); int customStart = r.getAlignmentStart();