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No changes, just sync-ing; only some commented out debugging prints are added... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2583 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-01-14 17:45:15 +00:00
parent d85461c463
commit df63f51253
1 changed files with 4 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
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@ -112,12 +112,15 @@ class ReferenceOrderedDataPool extends ResourcePool<SeekableRODIterator,Seekable
throw new StingException("Reference-ordered data cannot utilitize unmapped segments."); throw new StingException("Reference-ordered data cannot utilitize unmapped segments.");
GenomeLoc position = ((MappedStreamSegment)segment).locus; GenomeLoc position = ((MappedStreamSegment)segment).locus;
//#########################################
//## System.out.printf("Searching for iterator at locus %s; %d resources available%n", position, resources.size());
for( SeekableRODIterator iterator: resources ) { for( SeekableRODIterator iterator: resources ) {
//##System.out.printf("Examining iterator at position %s [last query location: %s]%n", iterator.position(),iterator.lastQueryLocation());
if( (iterator.position() == null && iterator.hasNext()) || if( (iterator.position() == null && iterator.hasNext()) ||
(iterator.position() != null && iterator.position().isBefore(position)) ) (iterator.position() != null && iterator.position().isBefore(position)) )
return iterator; return iterator;
} }
//##System.out.printf("Failed to find iterator at locus %s%n", position);
return null; return null;
} }