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Fix for JamesP's issue. This issue appeared because of a design flaw in the 

interface between SAMDataSource and IntervalSharder that needs to stay around
until the original BAM sharder is retired.  Will add a JIRA to fix design
flaw.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5661 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-04-19 00:52:13 +00:00
parent 50e86cfee9
commit 49550e257f
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
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@ -108,7 +108,8 @@ class FilePointer {
while(thisIterator.hasNext()) { while(thisIterator.hasNext()) {
// If there are no elements left in the 'other' iterator, spin out this iterator. // If there are no elements left in the 'other' iterator, spin out this iterator.
if(!otherIterator.hasNext()) { if(!otherIterator.hasNext()) {
difference += ((GATKBAMFileSpan)thisIterator.next()).size(); GATKBAMFileSpan nextSpan = (GATKBAMFileSpan)thisIterator.next().getValue();
difference += nextSpan.size();
continue; continue;
} }