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bug fixed; this rod seems to work now... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@826 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-05-26 22:25:34 +00:00
parent c72601322a
commit b81135c606
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/refdata/rodRefSeq.java
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@ -127,7 +127,10 @@ class refSeqIterator implements Iterator<rodRefSeq> {
Iterator<RefSeqRecord> i = records.iterator();
while ( i.hasNext() ) {
RefSeqRecord r = i.next();
if ( r.getLocation().getStop() < curr_position ) i.remove(); // we moved past the end of transcript r, purge it forever
if ( r.getLocation().getStop() < curr_position ) {
System.out.println("Throwing away: " + r.toString());
i.remove(); // we moved past the end of transcript r, purge it forever
}
}
} else {
// ooops, we are past the end of all loaded transcripts - kill them all,
@ -151,6 +154,7 @@ class refSeqIterator implements Iterator<rodRefSeq> {
if ( ci1 > ci2 ) throw new StingException("RefSeq track seems to be not contig-ordered");
if ( ci1 < ci2 ) break; // next transcript is on the next contig, we do not need it yet...
if ( r.getLocation().getStart() > curr_position ) break; // next transcript is on the same contig but starts after the current position; we are done
r = reader.next(); // we need next record, time to load it for real
long stop = r.getLocation().getStop();
if ( stop < curr_position ) throw new StingException("DEBUG: encuntered contig that should have been loaded earlier");
if ( stop > max_position ) max_position = stop;