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Fix hanging bug reported by Susanne Pfeifer (tiffy @ get satisfaction) where, if the last read(s) in a shard all have an 

indel in roughly the same location and that indel isn't covered by any other reads, LocusIteratorByState goes into an infinite
loop.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3348 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-05-11 17:31:19 +00:00
parent 34969f304c
commit 6868ce988f
1 changed files with 20 additions and 13 deletions
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33
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -250,6 +250,7 @@ public class LocusIteratorByState extends LocusIterator {
//final boolean DEBUG = false;
//final boolean DEBUG2 = false && DEBUG;
private Reads readInfo;
private AlignmentContext nextAlignmentContext;
// -----------------------------------------------------------------------------------------------------------------
//
@ -271,7 +272,8 @@ public class LocusIteratorByState extends LocusIterator {
}
public boolean hasNext() {
boolean r = ! readStates.isEmpty() || it.hasNext();
lazyLoadNextAlignmentContext();
boolean r = (nextAlignmentContext != null);
//if ( DEBUG ) System.out.printf("hasNext() = %b%n", r);
// if we don't have a next record, make sure we clean the warning queue
@ -303,12 +305,20 @@ public class LocusIteratorByState extends LocusIterator {
//
// -----------------------------------------------------------------------------------------------------------------
public AlignmentContext next() {
// keep iterating forward until we encounter a reference position that has something "real" hanging over it
// (i.e. either a real base, or a real base or a deletion if includeReadsWithDeletion is true)
while(true) {
lazyLoadNextAlignmentContext();
if(!hasNext())
throw new NoSuchElementException("LocusIteratorByState: out of elements.");
AlignmentContext currentAlignmentContext = nextAlignmentContext;
nextAlignmentContext = null;
return currentAlignmentContext;
}
/**
* Creates the next alignment context from the given state. Note that this is implemented as a lazy load method.
* nextAlignmentContext MUST BE null in order for this method to advance to the next entry.
*/
private void lazyLoadNextAlignmentContext() {
while(nextAlignmentContext == null && (!readStates.isEmpty() || it.hasNext())) {
// this call will set hasExtendedEvents to true if it picks up a read with indel right before the current position on the ref:
collectPendingReads(readInfo.getMaxReadsAtLocus());
@ -318,12 +328,12 @@ public class LocusIteratorByState extends LocusIterator {
int nMQ0Reads = 0;
// if extended events are requested, and if previous traversal step brought us over an indel in
// if extended events are requested, and if previous traversal step brought us over an indel in
// at least one read, we emit extended pileup (making sure that it is associated with the previous base,
// i.e. the one right *before* the indel) and do NOT shift the current position on the ref.
// In this case, the subsequent call to next() will emit the normal pileup at the current base
// and shift the position.
if ( readInfo.generateExtendedEvents() && hasExtendedEvents ) {
if (readInfo.generateExtendedEvents() && hasExtendedEvents) {
ArrayList<ExtendedEventPileupElement> indelPile = new ArrayList<ExtendedEventPileupElement>(readStates.size());
int maxDeletionLength = 0;
@ -370,12 +380,10 @@ public class LocusIteratorByState extends LocusIterator {
GenomeLoc loc = GenomeLocParser.incPos(our1stState.getLocation(),-1);
// System.out.println("Indel(s) at "+loc);
// for ( ExtendedEventPileupElement pe : indelPile ) { if ( pe.isIndel() ) System.out.println(" "+pe.toString()); }
return new AlignmentContext(loc, new ReadBackedExtendedEventPileup(loc, indelPile, size, maxDeletionLength, nInsertions, nDeletions, nMQ0Reads));
nextAlignmentContext = new AlignmentContext(loc, new ReadBackedExtendedEventPileup(loc, indelPile, size, maxDeletionLength, nInsertions, nDeletions, nMQ0Reads));
} else {
ArrayList<PileupElement> pile = new ArrayList<PileupElement>(readStates.size());
// todo -- performance problem -- should be lazy, really
for ( SAMRecordState state : readStates ) {
if ( state.getCurrentCigarOperator() != CigarOperator.D && state.getCurrentCigarOperator() != CigarOperator.N ) {
@ -398,9 +406,8 @@ public class LocusIteratorByState extends LocusIterator {
GenomeLoc loc = getLocation();
updateReadStates(); // critical - must be called after we get the current state offsets and location
// if we got reads with non-D/N over the current position, we are done
if ( pile.size() != 0 ) return new AlignmentContext(loc, new ReadBackedPileup(loc, pile, size, nDeletions, nMQ0Reads));
if ( pile.size() != 0 ) nextAlignmentContext = new AlignmentContext(loc, new ReadBackedPileup(loc, pile, size, nDeletions, nMQ0Reads));
}
}
}