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Probable patch to Jerry Glenn's GetSatisfaction report. I'm having him test it out. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5456 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-03-17 16:00:50 +00:00
parent 3eea6e92b7
commit 481750cbf9
1 changed files with 13 additions and 7 deletions
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20
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -184,6 +184,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// the current interval in the list // the current interval in the list
private GenomeLoc currentInterval = null; private GenomeLoc currentInterval = null;
private boolean sawReadInCurrentInterval = false;
// the reads and known indels that fall into the current interval // the reads and known indels that fall into the current interval
private final ReadBin readsToClean = new ReadBin(); private final ReadBin readsToClean = new ReadBin();
@ -428,12 +429,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( readLoc.getStop() == 0 ) if ( readLoc.getStop() == 0 )
readLoc = getToolkit().getGenomeLocParser().createGenomeLoc(readLoc.getContig(), readLoc.getStart(), readLoc.getStart()); readLoc = getToolkit().getGenomeLocParser().createGenomeLoc(readLoc.getContig(), readLoc.getStart(), readLoc.getStart());
if ( readLoc.isBefore(currentInterval) || ReadUtils.is454Read(read) ) { if ( readLoc.isBefore(currentInterval) ) {
// TODO -- it would be nice if we could use indels from 454 reads as alternate consenses if ( !sawReadInCurrentInterval )
emit(read); emit(read);
return 0; else
readsNotToClean.add(read);
} }
else if ( readLoc.overlapsP(currentInterval) ) { else if ( readLoc.overlapsP(currentInterval) ) {
sawReadInCurrentInterval = true;
if ( doNotTryToClean(read) ) { if ( doNotTryToClean(read) ) {
readsNotToClean.add(read); readsNotToClean.add(read);
} else { } else {
@ -458,7 +462,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
private void abortCleanForCurrentInterval() { private void abortCleanForCurrentInterval() {
emitReadLists(); emitReadLists();
currentInterval = intervals.hasNext() ? intervals.next() : null; currentInterval = intervals.hasNext() ? intervals.next() : null;
sawReadInCurrentInterval = false;
} }
private boolean doNotTryToClean(SAMRecord read) { private boolean doNotTryToClean(SAMRecord read) {
@ -467,7 +471,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
read.getReadFailsVendorQualityCheckFlag() || read.getReadFailsVendorQualityCheckFlag() ||
read.getMappingQuality() == 0 || read.getMappingQuality() == 0 ||
read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START || read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
ConstrainedMateFixingManager.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT); ConstrainedMateFixingManager.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT) ||
ReadUtils.is454Read(read);
// TODO -- it would be nice if we could use indels from 454 reads as alternate consenses
} }
private void cleanAndCallMap(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) { private void cleanAndCallMap(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
@ -488,7 +494,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
} catch (ReviewedStingException e) { } catch (ReviewedStingException e) {
throw new UserException.MissortedFile(new File(intervalsFile), " *** Are you sure that your interval file is sorted? If not, you must use the --targetIntervalsAreNotSorted argument. ***", e); throw new UserException.MissortedFile(new File(intervalsFile), " *** Are you sure that your interval file is sorted? If not, you must use the --targetIntervalsAreNotSorted argument. ***", e);
} }
sawReadInCurrentInterval = false;
// call back into map now that the state has been updated // call back into map now that the state has been updated
map(ref, read, metaDataTracker); map(ref, read, metaDataTracker);