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ReadShard.getReadsSpan(): handle case where shard contains only unmapped mates 

Nasty, nasty bug -- if we were extremely unlucky with shard boundaries, we might
end up with a shard containing only unmapped mates of mapped reads. In this case,
ReadShard.getReadsSpan() would not behave correctly, since the shard as a whole would
be marked "mapped" (since it refers to mapped intervals) yet consist only of unmapped
mates of mapped reads located within those intervals.
This commit is contained in:
David Roazen 2012-10-02 13:43:01 -04:00
parent 9a8f53e76c
commit a96ed385df
1 changed files with 13 additions and 3 deletions
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16
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
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@ -215,19 +215,29 @@ public class ReadShard extends Shard {
int start = Integer.MAX_VALUE; int start = Integer.MAX_VALUE;
int stop = Integer.MIN_VALUE; int stop = Integer.MIN_VALUE;
String contig = null; String contig = null;
boolean foundMapped = false;
for ( final SAMRecord read : reads ) { for ( final SAMRecord read : reads ) {
if ( contig != null && ! read.getReferenceName().equals(contig) ) if ( contig != null && ! read.getReferenceName().equals(contig) )
throw new ReviewedStingException("ReadShard contains reads spanning contig boundaries, which is no longer allowed. " throw new ReviewedStingException("ReadShard contains reads spanning contig boundaries, which is no longer allowed. "
+ "First contig is " + contig + " next read was " + read.getReferenceName() ); + "First contig is " + contig + " next read was " + read.getReferenceName() );
contig = read.getReferenceName(); contig = read.getReferenceName();
if ( read.getAlignmentStart() < start ) start = read.getAlignmentStart();
if ( read.getAlignmentEnd() > stop ) stop = read.getAlignmentEnd(); // Even if this shard as a *whole* is not "unmapped", we can still encounter *individual* unmapped mates
// of mapped reads within this shard's buffer. In fact, if we're very unlucky with shard boundaries,
// this shard might consist *only* of unmapped mates! We need to refrain from using the alignment
// starts/stops of these unmapped mates, and detect the case where the shard has been filled *only*
// with unmapped mates.
if ( ! read.getReadUnmappedFlag() ) {
foundMapped = true;
if ( read.getAlignmentStart() < start ) start = read.getAlignmentStart();
if ( read.getAlignmentEnd() > stop ) stop = read.getAlignmentEnd();
}
} }
assert contig != null; assert contig != null;
if ( contig.equals("*") ) // all reads are unmapped if ( ! foundMapped || contig.equals("*") ) // all reads are unmapped
return GenomeLoc.UNMAPPED; return GenomeLoc.UNMAPPED;
else else
return parser.createGenomeLoc(contig, start, stop); return parser.createGenomeLoc(contig, start, stop);