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Fix sharding bug -- loci to which >100,000 (= 1 shard) reads are assigned an 

alignment start will confuse the sharding system and cause it to return duplicate reads.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1987 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-11-08 14:27:26 +00:00
parent f777c806d6
commit 21c5f543fa
1 changed files with 8 additions and 7 deletions
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15
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
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@ -294,12 +294,16 @@ public class SAMDataSource implements SimpleDataSource {
} }
int x = 0; int x = 0;
SAMRecord rec = null; SAMRecord rec = null;
int lastPos = 0;
// Assuming that lastReadPos should never be null, because this is a mappedReadSeek
// and initial queries are handled by the previous conditional.
int lastContig = lastReadPos.getContigIndex();
int lastPos = (int)lastReadPos.getStart();
while (x < readsTaken) { while (x < readsTaken) {
if (iter.hasNext()) { if (iter.hasNext()) {
rec = iter.next(); rec = iter.next();
if (lastPos == rec.getAlignmentStart()) ++this.readsSeenAtLastPos; if (lastContig == rec.getReferenceIndex() && lastPos == rec.getAlignmentStart()) ++this.readsSeenAtLastPos;
else this.readsSeenAtLastPos = 1; else this.readsSeenAtLastPos = 1;
lastPos = rec.getAlignmentStart(); lastPos = rec.getAlignmentStart();
++x; ++x;
@ -368,12 +372,9 @@ public class SAMDataSource implements SimpleDataSource {
private void correctForReadPileupSeek( StingSAMIterator iter ) { private void correctForReadPileupSeek( StingSAMIterator iter ) {
// move the number of reads we read from the last pos // move the number of reads we read from the last pos
boolean atLeastOneReadSeen = false; // we have a problem where some chomesomes don't have a single read (i.e. the chrN_random chrom.) boolean atLeastOneReadSeen = false; // we have a problem where some chomesomes don't have a single read (i.e. the chrN_random chrom.)
while (iter.hasNext() && this.readsSeenAtLastPos > 0) { for(int i = 0; i < this.readsSeenAtLastPos && iter.hasNext(); i++,iter.next())
iter.next();
--readsSeenAtLastPos;
atLeastOneReadSeen = true; atLeastOneReadSeen = true;
} if (readsSeenAtLastPos > 0 && !atLeastOneReadSeen) {
if (readsSeenAtLastPos != 0 && atLeastOneReadSeen) {
throw new SimpleDataSourceLoadException("Seek problem: reads at last position count != 0"); throw new SimpleDataSourceLoadException("Seek problem: reads at last position count != 0");
} }
} }