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In reference traversals, this view did not expect a possibility of TWO alignment contexts (base pileup followed by extended event pileup) associated with the same location. As the result, extended event pileups were silently skipped even when enabled in the traversal engine. Fixed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2970 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-03-09 22:18:44 +00:00
parent bc3761dc16
commit c638c29eea
1 changed files with 23 additions and 9 deletions
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32
java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
View File

@ -30,13 +30,13 @@ public class AllLocusView extends LocusView {
private GenomeLocusIterator locusIterator;
/**
* Gets the current position in the view.
* Gets the next position in the view: next call to next() will jump there.
* Note that both nextPosition and nextLocus are PRE-read and cached.
*/
private GenomeLoc nextPosition = null;
/**
* What's the context for the last locus accessed?
* @param provider
* What's the next available context?
*/
private AlignmentContext nextLocus = null;
@ -49,6 +49,7 @@ public class AllLocusView extends LocusView {
// Seed the state tracking members with the first possible seek position and the first possible locus context.
locusIterator = new GenomeLocusIterator(provider.getLocus());
if( locusIterator.hasNext() ) {
// cache next position and next alignment context
nextPosition = locusIterator.next();
nextLocus = hasNextLocus() ? nextLocus() : createEmptyLocus(nextPosition);
}
@ -59,22 +60,35 @@ public class AllLocusView extends LocusView {
}
public AlignmentContext next() {
GenomeLoc currentPosition = nextPosition;
if( currentPosition == null )
throw new NoSuchElementException("No next is available in the all locus view");
// Determine the next locus.
nextPosition = locusIterator.hasNext() ? locusIterator.next() : null;
// Crank the iterator to (if possible) or past the next context.
while( nextLocus != null && nextLocus.getLocation().isBefore(currentPosition) && hasNextLocus() )
nextLocus = nextLocus();
AlignmentContext currentLocus = null; // context we are gonna return
// If actual data is present, return it. Otherwise, return empty data.
if( nextLocus != null && nextLocus.getLocation().equals(currentPosition) )
return nextLocus;
if( nextLocus != null && nextLocus.getLocation().equals(currentPosition) ) {
currentLocus = nextLocus; // found alignment context at the current position
nextLocus = hasNextLocus() ? nextLocus() : null;
}
else
return createEmptyLocus( currentPosition );
currentLocus = createEmptyLocus( currentPosition );
// Determine the next locus. The trick is that we may have more than one alignment context at the same
// reference position (regular base pileup, then extended pileup). If next alignment context (that we just pre-read)
// is still at the current position, we do not increment current position and wait for next call to next() to return
// that context. If we know that next context is past the current position, we are done with current
// position
if ( nextLocus == null || ! nextLocus.getLocation().equals(currentPosition) )
nextPosition = locusIterator.hasNext() ? locusIterator.next() : null;
return currentLocus;
}
@Override