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a fix for a situation where a chromosome on the reference file contains no reads, and doesn't align to the bam file. This came up using reference 18, which has chomosomes like chr1_random that aren't in all BAM files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@649 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-05-11 01:39:25 +00:00
parent ee02b61068
commit 8d43ec3d7e
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
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@ -285,11 +285,13 @@ public class SAMDataSource implements SimpleDataSource {
iter.queryContained(lastReadPos.getContig(), (int) lastReadPos.getStop(), -1); iter.queryContained(lastReadPos.getContig(), (int) lastReadPos.getStop(), -1);
// 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.)
while (iter.hasNext() && this.readsAtLastPos > 0) { while (iter.hasNext() && this.readsAtLastPos > 0) {
iter.next(); iter.next();
--readsAtLastPos; --readsAtLastPos;
atLeastOneReadSeen = true;
} }
if (readsAtLastPos != 0) { if (readsAtLastPos != 0 && atLeastOneReadSeen) {
throw new SimpleDataSourceLoadException("Seek problem: reads at last position count != 0"); throw new SimpleDataSourceLoadException("Seek problem: reads at last position count != 0");
} }