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Fix for old, broken invariant where unmapped reads are represented by null rather than an empty BAMFileSpan. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5819 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2011-05-18 20:57:38 +00:00
parent ebcd333ed8
commit a38b2be329
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
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@ -94,7 +94,7 @@ public class BAMScheduler implements Iterator<FilePointer> {
if(currentLocus == GenomeLoc.UNMAPPED) { if(currentLocus == GenomeLoc.UNMAPPED) {
nextFilePointer = new FilePointer(GenomeLoc.UNMAPPED); nextFilePointer = new FilePointer(GenomeLoc.UNMAPPED);
for(SAMReaderID id: dataSource.getReaderIDs()) for(SAMReaderID id: dataSource.getReaderIDs())
nextFilePointer.addFileSpans(id,null); nextFilePointer.addFileSpans(id,new GATKBAMFileSpan());
currentLocus = null; currentLocus = null;
continue; continue;
} }