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Fix exception in block weighting minus function. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5628 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2011-04-13 17:07:04 +00:00
parent 9ee30ce594
commit 5849e112e1
1 changed files with 8 additions and 1 deletions
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9
java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
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@ -105,7 +105,14 @@ class FilePointer {
PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>> thisIterator = new PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>>(this.fileSpans.entrySet().iterator()); PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>> thisIterator = new PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>>(this.fileSpans.entrySet().iterator());
PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>> otherIterator = new PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>>(other.fileSpans.entrySet().iterator()); PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>> otherIterator = new PeekableIterator<Map.Entry<SAMReaderID,SAMFileSpan>>(other.fileSpans.entrySet().iterator());
while(thisIterator.hasNext() || otherIterator.hasNext()) { while(thisIterator.hasNext()) {
// If there are no elements left in the 'other' iterator, spin out this iterator.
if(!otherIterator.hasNext()) {
difference += ((GATKBAMFileSpan)thisIterator.next()).size();
continue;
}
// Otherwise, compare the latest value.
int compareValue = thisIterator.peek().getKey().compareTo(otherIterator.peek().getKey()); int compareValue = thisIterator.peek().getKey().compareTo(otherIterator.peek().getKey());
if(compareValue < 0) { if(compareValue < 0) {