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Merge pull request #27 from broadinstitute/rp_ranksumtest_optimization 

Optimization to ReadPosRankSumTest: Don't do the work of parsing through...
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depristo 2013-02-11 08:58:22 -08:00
parent f8e2153c71 3f2f837b6a
commit 59484dfae4
1 changed files with 4 additions and 7 deletions
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11
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
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@ -103,6 +103,10 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
} }
for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : alleleLikelihoodMap.getLikelihoodReadMap().entrySet()) { for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : alleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
final Allele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
if (a.isNoCall())
continue; // read is non-informative
final GATKSAMRecord read = el.getKey(); final GATKSAMRecord read = el.getKey();
final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true ); final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true );
if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED || read.getCigar() == null ) if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED || read.getCigar() == null )
@ -112,17 +116,10 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
if (readPos > numAlignedBases / 2) if (readPos > numAlignedBases / 2)
readPos = numAlignedBases - (readPos + 1); readPos = numAlignedBases - (readPos + 1);
// int readPos = getOffsetFromClippedReadStart(el.getKey(), el.getKey().getOffset());
// readPos = getFinalReadPosition(el.getKey().getRead(),readPos);
final Allele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
if (a.isNoCall())
continue; // read is non-informative
if (a.isReference()) if (a.isReference())
refQuals.add((double)readPos); refQuals.add((double)readPos);
else if (allAlleles.contains(a)) else if (allAlleles.contains(a))
altQuals.add((double)readPos); altQuals.add((double)readPos);
} }
} }