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Minor optimizations to avoid extra processing (esp. for reduced reads)

This commit is contained in:
Eric Banks 2011-12-27 13:16:25 -05:00
parent dd990061f6
commit adff40ff58
1 changed files with 7 additions and 4 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -275,19 +275,22 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
public int add(PileupElement elt, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) { public int add(PileupElement elt, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
byte obsBase = elt.getBase(); byte obsBase = elt.getBase();
byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual); byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
if ( qual == 0 )
return 0;
if ( elt.isReducedRead() ) { if ( elt.isReducedRead() ) {
// reduced read representation // reduced read representation
if ( BaseUtils.isRegularBase( obsBase )) { if ( BaseUtils.isRegularBase( obsBase )) {
add(obsBase, qual, (byte)0, (byte)0, elt.getRepresentativeCount()); // fast calculation of n identical likelihoods int representativeCount = elt.getRepresentativeCount();
return elt.getRepresentativeCount(); // we added nObs bases here add(obsBase, qual, (byte)0, (byte)0, representativeCount); // fast calculation of n identical likelihoods
return representativeCount; // we added nObs bases here
} }
// odd bases or deletions => don't use them // odd bases or deletions => don't use them
return 0; return 0;
} }
return qual > 0 ? add(obsBase, qual, (byte)0, (byte)0, 1) : 0; return add(obsBase, qual, (byte)0, (byte)0, 1);
} }
public int add(List<PileupElement> overlappingPair, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) { public int add(List<PileupElement> overlappingPair, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
@ -519,7 +522,7 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
if ( qual > SAMUtils.MAX_PHRED_SCORE ) if ( qual > SAMUtils.MAX_PHRED_SCORE )
throw new UserException.MalformedBAM(p.getRead(), String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s. Perhaps your BAM incorrectly encodes the quality scores in Sanger format; see http://en.wikipedia.org/wiki/FASTQ_format for more details", SAMUtils.MAX_PHRED_SCORE, qual, p.getRead().getReadName())); throw new UserException.MalformedBAM(p.getRead(), String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s. Perhaps your BAM incorrectly encodes the quality scores in Sanger format; see http://en.wikipedia.org/wiki/FASTQ_format for more details", SAMUtils.MAX_PHRED_SCORE, qual, p.getRead().getReadName()));
if ( capBaseQualsAtMappingQual ) if ( capBaseQualsAtMappingQual )
qual = (byte)Math.min((int)p.getQual(), p.getMappingQual()); qual = (byte)Math.min((int)qual, p.getMappingQual());
if ( (int)qual < minBaseQual ) if ( (int)qual < minBaseQual )
qual = (byte)0; qual = (byte)0;