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1) now is tolerant to sloppy cigar strings with 0-length elements (at the price of extra recursive call) 

2) when reads with deletions are requested, adds to the pile just those: reads with 'D' over the current reference base, but not 'N'
3) next() now implements a loop: recursive forward iteration calls to next() until ref. position with non-zero coverage is encountered were OK for (short) deletions, but with long stretches of N's they end up with stack overflow

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1568 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-09-09 20:04:04 +00:00
parent 542af6402e
commit dd0085c428
1 changed files with 26 additions and 18 deletions
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44
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -113,11 +113,14 @@ public class LocusIteratorByState extends LocusIterator {
// return null; // we are done
//if (DEBUG2) System.out.printf("stepForwardOnGenome2: curElement=%s, counter=%d, len=%d%n", curElement, cigarElementCounter, curElement != null ? curElement.getLength() : -1);
if ( curElement == null || ++cigarElementCounter >= curElement.getLength() ) {
if ( curElement == null || ++cigarElementCounter > curElement.getLength() ) {
cigarOffset++;
if ( cigarOffset < nCigarElements ) {
curElement = cigar.getCigarElement(cigarOffset);
cigarElementCounter = 0;
// next line: guards against cigar elements of length 0; when new cigar element is retrieved,
// we reenter in order to re-check cigarElementCounter against curElement's length
return stepForwardOnGenome();
} else {
return null;
}
@ -215,31 +218,36 @@ public class LocusIteratorByState extends LocusIterator {
// printState();
//}
collectPendingReads(readInfo.getMaxReadsAtLocus());
// todo -- performance problem -- should be lazy, really
ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>(readStates.size());
ArrayList<Integer> offsets = new ArrayList<Integer>(readStates.size());
for ( SAMRecordState state : readStates ) {
if ( state.getCurrentCigarOperator() != CigarOperator.D && state.getCurrentCigarOperator() != CigarOperator.N ) {
// System.out.println("Location: "+getLocation()+"; Read "+state.getRead().getReadName()+"; offset="+state.getReadOffset());
reads.add(state.getRead());
offsets.add(state.getReadOffset());
} else if ( readInfo.includeReadsWithDeletionAtLoci() ) {
reads.add(state.getRead());
offsets.add(-1);
}
}
GenomeLoc loc = getLocation();
updateReadStates(); // critical - must be called after we get the current state offsets and location
// 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) {
collectPendingReads(readInfo.getMaxReadsAtLocus());
// todo -- performance problem -- should be lazy, really
for ( SAMRecordState state : readStates ) {
if ( state.getCurrentCigarOperator() != CigarOperator.D && state.getCurrentCigarOperator() != CigarOperator.N ) {
// System.out.println("Location: "+getLocation()+"; Read "+state.getRead().getReadName()+"; offset="+state.getReadOffset());
reads.add(state.getRead());
offsets.add(state.getReadOffset());
} else if ( readInfo.includeReadsWithDeletionAtLoci() && state.getCurrentCigarOperator() != CigarOperator.N ) {
reads.add(state.getRead());
offsets.add(-1);
}
}
GenomeLoc loc = getLocation();
updateReadStates(); // critical - must be called after we get the current state offsets and location
//if (DEBUG) {
// logger.debug("DONE WITH NEXT, updating read states, current state is:");
// printState();
//}
return reads.size() == 0 ? next() : new AlignmentContext(loc, reads, offsets);
// if we got reads with non-D/N over the current position, we are done
if ( reads.size() != 0 ) return new AlignmentContext(loc, reads, offsets);
}
}
private void collectPendingReads(final int maximumPileupSize) {