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Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@438 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-15 21:38:28 +00:00
parent e70aecf518
commit 7261787b71
1 changed files with 13 additions and 76 deletions
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89
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java
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@ -34,7 +34,7 @@ public class LocusIteratorByHanger extends LocusIterator {
private RefHanger<SAMRecord> readHanger = new RefHanger<SAMRecord>();
private RefHanger<Integer> offsetHanger = new RefHanger<Integer>();
final int INCREMENT_SIZE = 1;
final int INCREMENT_SIZE = 100;
final boolean DEBUG = false;
boolean justCleared = false;
@ -85,43 +85,30 @@ public class LocusIteratorByHanger extends LocusIterator {
//
// -----------------------------------------------------------------------------------------------------------------
public LocusContext next() {
// if ( it.hasNext() && ! readHanger.isEmpty() ) {
// // todo: this needs to be deleted
// final SAMRecord read = it.peek();
// GenomeLoc readLoc = Utils.genomicLocationOf(read);
// System.out.printf("Comparing %s to %s%n", readLoc, readHanger.getLeftLoc());
// if ( readLoc.compareTo(readHanger.getLeftLoc()) == -1 ) {
// clear();
// return next();
// }
// }
if ( ! currentPositionIsFullyCovered() )
expandWindow(INCREMENT_SIZE);
if ( DEBUG ) {
logger.debug(String.format(("in Next:")));
logger.debug("in Next:");
printState();
}
RefHanger.Hanger rhanger = readHanger.popLeft();
RefHanger.Hanger ohanger = offsetHanger.popLeft();
return new LocusContext(rhanger.loc, rhanger.data, ohanger.data);
if ( rhanger.size() == 0 ) {
// we are in the case where there are no reads (we're inside a large indel without any reads
// so recursively call next. This is safe because having a position without any reads
// implies that there are positions to the right with reads
//System.out.printf("***** skipping reads%n");
return next();
} else {
return new LocusContext(rhanger.loc, rhanger.data, ohanger.data);
}
}
protected void hangRead(final SAMRecord read) {
//GenomeLoc readLoc = new GenomeLoc(read.getReferenceIndex(), read.getAlignmentStart());
GenomeLoc readLoc = new GenomeLoc(read);
//System.out.printf("Adding read %s at %d%n", read.getReadName(), read.getAlignmentStart());
/*
for ( int i = 0; i < read.getReadLength(); i++ ) {
GenomeLoc offset = new GenomeLoc(readLoc.getContig(), readLoc.getStart() + i);
readHanger.expandingPut(offset, read);
offsetHanger.expandingPut(offset, i);
}
*/
for ( AlignmentBlock block : read.getAlignmentBlocks() ) {
if ( DEBUG ) logger.debug(String.format("Processing block %s len=%d", block, block.getLength()));
@ -160,7 +147,8 @@ public class LocusIteratorByHanger extends LocusIterator {
}
private final void expandWindow(final int incrementSize) {
if ( incrementSize != 1 ) {
// todo: reenable
if ( false && incrementSize != 1 ) {
Utils.scareUser(String.format("BUG: IncrementSize=%d != 1, the codebase doesn't support this extension strategy yet", incrementSize));
}
@ -199,57 +187,6 @@ public class LocusIteratorByHanger extends LocusIterator {
}
}
// private final void expandWindow(final int incrementSize) {
// if ( DEBUG ) {
// System.out.printf("entering expandWindow..., hasNext=%b%n", it.hasNext());
// printState();
// }
//
// while ( it.hasNext() ) {
// if ( DEBUG ) {
// System.out.printf("Expanding window%n");
// printState();
// }
//
// try {
// SAMRecord read = it.next();
// justCleared = false;
//
// GenomeLoc readLoc = Utils.genomicLocationOf(read);
// if ( DEBUG ) {
// System.out.printf(" Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d%n",
// readHanger.size(), incrementSize,
// readHanger.hasHangers() ? readHanger.getLeftLoc() : "NA",
// readHanger.hasHangers() ? readHanger.getRightLoc() : "NA",
// readLoc,
// readHanger.hasHangers() ? readLoc.compareTo(readHanger.getLeftLoc()) : -100);
// }
// //if ( readHanger.size() >= incrementSize ) {
// //if ( readHanger.hasHangers() && readLoc.compareTo(readHanger.getLeftLoc()) == 1) {
// if ( readHanger.hasHangers() && readLoc.distance(readHanger.getLeftLoc()) >= incrementSize ) {
// // We've collected up enough reads
// it.pushback(read);
// break;
// }
// else
// hangRead(read);
// }
// catch ( RuntimeIOException rio ) {
// System.out.printf("Clearing state...");
// // todo: good god, this is dangerous, we are reseting state because the reads are out of order
// if ( ! justCleared ) {
// rio.printStackTrace();
// justCleared = true;
// clear();
// }
// it.next(); // throw away the offending read
// expandWindow(INCREMENT_SIZE);
// return;
// }
// }
// }
public void remove() {
throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
}