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Optimization: create allele list just once, not for each genotype

This commit is contained in:
Eric Banks 2012-03-02 13:30:17 -05:00
parent 0a7137616c
commit 1e07e97b58
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -43,15 +43,15 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
final ArrayList<Double> altQuals = new ArrayList<Double>(); final ArrayList<Double> altQuals = new ArrayList<Double>();
if ( vc.isSNP() ) { if ( vc.isSNP() ) {
final List<Byte> altAlleles = new ArrayList<Byte>();
for ( final Allele a : vc.getAlternateAlleles() )
altAlleles.add(a.getBases()[0]);
for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) { for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {
final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName()); final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
if ( context == null ) if ( context == null )
continue; continue;
final List<Byte> altAlleles = new ArrayList<Byte>();
for ( final Allele a : vc.getAlternateAlleles() )
altAlleles.add(a.getBases()[0]);
fillQualsFromPileup(ref.getBase(), altAlleles, context.getBasePileup(), refQuals, altQuals); fillQualsFromPileup(ref.getBase(), altAlleles, context.getBasePileup(), refQuals, altQuals);
} }
} else if ( vc.isIndel() || vc.isMixed() ) { } else if ( vc.isIndel() || vc.isMixed() ) {