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synchronyzing; debug statements commented out, so nothing changed really 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1215 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-07-10 16:38:33 +00:00
parent a1eb128377
commit b08b121756
1 changed files with 8 additions and 0 deletions
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8
java/src/org/broadinstitute/sting/gatk/refdata/rodRefSeq.java
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@ -151,8 +151,10 @@ class refSeqIterator implements Iterator<rodRefSeq> {
@Override
public rodRefSeq next() {
// if ( z == 0 ) t = System.currentTimeMillis();
// System.out.println("NEXT on REFSEQ ITERATOR");
curr_position++;
if ( curr_position <= max_position ) {
// we still have bases covered by at least one currently loaded transcript;
// we have to purge only subset of transcripts, on which we moved past the end
Iterator<Transcript> i = records.iterator();
@ -173,18 +175,23 @@ class refSeqIterator implements Iterator<rodRefSeq> {
max_position = t.getLocation().getStop();
}
// System.out.println("curr pos="+curr_position+"; max pos="+max_position);
// 'records' only keeps those transcripts now, on which we did not reach the end yet
// (we might have reloaded records completely if it was necessary); current position is correctly set.
// lets check if we walked into additional new transcripts so we'd need to load them too:
while ( reader.hasNext() ) {
Transcript t = reader.peek();
// System.out.println("next transcript at "+t.getLocation()+"; curr contig is "+curr_contig_name);
int ci1 = GenomeLocParser.getContigIndex(curr_contig_name);
int ci2 = GenomeLocParser.getContigIndex( t.getLocation().getContig() );
// System.out.println("Contigs: "+ci1+":"+ci2);
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 ( t.getLocation().getStart() > curr_position ) break; // next transcript is on the same contig but starts after the current position; we are done
t = reader.next(); // we do need next record, time to load it for real
// System.out.println("loaded next transcript");
long stop = t.getLocation().getStop();
if ( stop < curr_position ) throw new StingException("DEBUG: encountered contig that should have been loaded earlier");
if ( stop > max_position ) max_position = stop;
@ -194,6 +201,7 @@ class refSeqIterator implements Iterator<rodRefSeq> {
// 'records' and current position are fully updated. We can now create new rod and return it (NOTE: this iterator will break if the list
// of pre-loaded records is meddled with by the clients between iterations, so we return them as unmodifiable list)
rodRefSeq rod = new rodRefSeq(name, GenomeLocParser.parseGenomeLoc(curr_contig_name,curr_position, curr_position),Collections.unmodifiableList(records));
// System.out.println("Returning rod at "+rod.getLocation());
// if ( (++z) % 1000000 == 0 ) {
// System.out.println(rod.getLocation()+": holding "+records.size()+ "; time per 1M ref positions: "+((double)(System.currentTimeMillis()-t)/1000.0)+" s");
// z = 0;