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More excessively micro micro-optimizations #5616

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merged 4 commits into from
Feb 8, 2019
Merged

More excessively micro micro-optimizations #5616

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b194fab
replaced some iterators with indexed-for-lists in hopes of making an …
jamesemery Jan 28, 2019
4b8941b
responded to comments
jamesemery Feb 7, 2019
7881211
fixing the error
jamesemery Feb 8, 2019
73d6f78
responding to final comments
jamesemery Feb 8, 2019
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24 changes: 17 additions & 7 deletions ...org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -193,18 +193,20 @@ public List<VariantContext> calculateRefConfidence(final Haplotype refHaplotype,
final String sampleName = readLikelihoods.getSample(0);

final int globalRefOffset = refSpan.getStart() - activeRegion.getExtendedSpan().getStart();
for ( final ReadPileup pileup : refPileups ) {
// Note, we use an indexed for-loop here because this method has a large impact on the profile of HaplotypeCaller runtime in GVCF mode
final int refPileupsSize = refPileups.size();
for (int i = 0; i < refPileupsSize; i++) {
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Add comment here that the old-school for loop is intentional (for-each was found to show up on the profiler).

final ReadPileup pileup = refPileups.get(i);
final Locatable curPos = pileup.getLocation();
final int offset = curPos.getStart() - refSpan.getStart();

final VariantContext overlappingSite = GATKVariantContextUtils.getOverlappingVariantContext(curPos, variantCalls);
final List<VariantContext> currentPriors = getMatchingPriors(curPos, overlappingSite, VCpriors);
if ( overlappingSite != null && overlappingSite.getStart() == curPos.getStart() ) {
final List<VariantContext> currentPriors = VCpriors.isEmpty() ? Collections.emptyList() : getMatchingPriors(curPos, overlappingSite, VCpriors);
if (overlappingSite != null && overlappingSite.getStart() == curPos.getStart()) {
if (applyPriors) {
results.add(PosteriorProbabilitiesUtils.calculatePosteriorProbs(overlappingSite, currentPriors,
numRefSamplesForPrior, options));
}
else {
} else {
results.add(overlappingSite);
}
} else {
Expand Down Expand Up @@ -420,9 +422,17 @@ protected static boolean isAltAfterAssembly(final PileupElement element, final b
* @param priorList priors within the current ActiveRegion
* @return prior VCs representing the same variant position as call
*/
List<VariantContext> getMatchingPriors(final Locatable curPos, final VariantContext call, final List<VariantContext> priorList) {
private List<VariantContext> getMatchingPriors(final Locatable curPos, final VariantContext call, final List<VariantContext> priorList) {
final int position = call != null ? call.getStart() : curPos.getStart();
return priorList.stream().filter(vc -> position == vc.getStart()).collect(Collectors.toList());
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Add a comment that this method is implemented with an old-school for loop instead of streaming for performance reasons (otherwise, someone will probably come along in 2 years and undo this).

final List<VariantContext> matchedPriors = new ArrayList<>(priorList.size());
// NOTE: a for loop is used here because this method ends up being called per-pileup, per-read and using a loop instead of streaming saves runtime
final int priorsListSize = priorList.size();
for (int i = 0; i < priorsListSize; i++) {
if (position == priorList.get(i).getStart()) {
matchedPriors.add(priorList.get(i));
}
}
return matchedPriors;
}

/**
Expand Down