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don't make mapping quality too high 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1066 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-21 04:51:42 +00:00
parent 686c8133ed
commit a21c2a7e48
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -360,13 +360,13 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// however we don't have enough info to use the proper MAQ scoring system.
// For now, we'll use a heuristic:
// the mapping quality score is improved by the LOD difference in mismatching
// bases between the reference and alternate consensus
// bases between the reference and alternate consensus (divided by 10)
// finish cleaning the appropriate reads
for ( Pair<Integer, Integer> indexPair : bestConsensus.readIndexes ) {
AlignedRead aRead = altReads.get(indexPair.first);
if ( aRead.finalizeUpdate() ) {
aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + (int)improvement, 255));
aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + (int)(improvement/10.0), 255));
aRead.getRead().setAttribute("NM", AlignmentUtils.numMismatches(aRead.getRead(), reference, aRead.getRead().getAlignmentStart()-(int)leftmostIndex));
}
}
@ -393,7 +393,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
for ( AlignedRead aRec : leftMovedIndels )
aRec.finalizeUpdate();
for ( AlignedRead aRec : altReads ) {
if ( aRec.wasUpdated() )
if ( !cleanedReadsOnly || aRec.wasUpdated() )
readsToWrite.add(new ComparableSAMRecord(aRec.getRead()));
}
}