zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -184,6 +184,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// the current interval in the list
private GenomeLoc currentInterval = null;
private boolean sawReadInCurrentInterval = false;
// the reads and known indels that fall into the current interval
private final ReadBin readsToClean = new ReadBin();
@ -428,12 +429,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( readLoc.getStop() == 0 )
readLoc = getToolkit().getGenomeLocParser().createGenomeLoc(readLoc.getContig(), readLoc.getStart(), readLoc.getStart());
if ( readLoc.isBefore(currentInterval) || ReadUtils.is454Read(read) ) {
// TODO -- it would be nice if we could use indels from 454 reads as alternate consenses
emit(read);
return 0;
if ( readLoc.isBefore(currentInterval) ) {
if ( !sawReadInCurrentInterval )
emit(read);
else
readsNotToClean.add(read);
}
else if ( readLoc.overlapsP(currentInterval) ) {
sawReadInCurrentInterval = true;
if ( doNotTryToClean(read) ) {
readsNotToClean.add(read);
} else {
@ -458,7 +462,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
private void abortCleanForCurrentInterval() {
emitReadLists();
currentInterval = intervals.hasNext() ? intervals.next() : null;
sawReadInCurrentInterval = false;
}
private boolean doNotTryToClean(SAMRecord read) {
@ -467,7 +471,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
read.getReadFailsVendorQualityCheckFlag() ||
read.getMappingQuality() == 0 ||
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) {
@ -488,7 +494,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
} 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);
}
sawReadInCurrentInterval = false;
// call back into map now that the state has been updated
map(ref, read, metaDataTracker);