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The cleaner now cleans duplicate reads (instead of ignoring them) - although it doesn't include them for scoring ref or alt consenses 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2424 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-21 21:01:55 +00:00
parent cf303810d3
commit f448a263e9
1 changed files with 5 additions and 7 deletions
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12
java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -111,8 +111,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
for ( SAMRecord read : reads ) { for ( SAMRecord read : reads ) {
if ( !read.getReadUnmappedFlag() && if ( !read.getReadUnmappedFlag() &&
!read.getNotPrimaryAlignmentFlag() && !read.getNotPrimaryAlignmentFlag() &&
!read.getDuplicateReadFlag() && read.getMappingQuality() != 0 &&
read.getMappingQuality() != 0 &&
read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START && read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START &&
(allow454 || !Utils.is454Read(read)) ) (allow454 || !Utils.is454Read(read)) )
goodReads.add(read); goodReads.add(read);
@ -121,9 +120,6 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
} }
clean(goodReads, ref, loc); clean(goodReads, ref, loc);
//bruteForceClean(goodReads, ref, context.getLocation().getStart());
//testCleanWithDeletion();
//testCleanWithInsertion();
if ( writer != null ) { if ( writer != null ) {
// Although we can guarantee that reads will be emitted in order WITHIN an interval // Although we can guarantee that reads will be emitted in order WITHIN an interval
@ -257,7 +253,8 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// if this doesn't match perfectly to the reference, let's try to clean it // if this doesn't match perfectly to the reference, let's try to clean it
if ( mismatchScore > 0 ) { if ( mismatchScore > 0 ) {
altReads.add(aRead); altReads.add(aRead);
totalMismatchSum += mismatchScore; if ( !read.getDuplicateReadFlag() )
totalMismatchSum += mismatchScore;
aRead.setMismatchScoreToReference(mismatchScore); aRead.setMismatchScoreToReference(mismatchScore);
// if it has an indel, let's see if that's the best consensus // if it has an indel, let's see if that's the best consensus
if ( numBlocks == 2 ) if ( numBlocks == 2 )
@ -325,7 +322,8 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
consensus.readIndexes.add(new Pair<Integer, Integer>(j, altAlignment.first)); consensus.readIndexes.add(new Pair<Integer, Integer>(j, altAlignment.first));
//logger.debug(consensus.str + " vs. " + toTest.getRead().getReadString() + " => " + myScore + " - " + altAlignment.first); //logger.debug(consensus.str + " vs. " + toTest.getRead().getReadString() + " => " + myScore + " - " + altAlignment.first);
consensus.mismatchSum += myScore; if ( !toTest.getRead().getDuplicateReadFlag() )
consensus.mismatchSum += myScore;
} }
//logger.debug(consensus.str + " " + consensus.mismatchSum); //logger.debug(consensus.str + " " + consensus.mismatchSum);