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Bug fix for the case of reads with no read bases! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4184 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-09-01 16:58:54 +00:00
parent 0c54bf4195
commit a975db2c2e
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -334,6 +334,10 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
*/
public SAMRecord map( ReferenceContext refBases, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
if( read.getReadLength() == 0 ) { // Some reads have '*' as the SEQ field and samtools returns length zero. We don't touch these reads.
return read;
}
RecalDataManager.parseSAMRecord( read, RAC );
byte[] originalQuals = read.getBaseQualities();