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Merge pull request #1544 from broadinstitute/rhl_thread_safety_1543 

Synchronize modification/access to practicalAlleleCountForPloidy
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Ron Levine 2017-01-07 10:00:18 -05:00 committed by GitHub
parent 7447616766 4f52395795
commit c5df90b598
1 changed files with 1 additions and 1 deletions
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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
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@ -353,7 +353,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<AssemblyBa
* @param ploidy ploidy of the sample * @param ploidy ploidy of the sample
* @param alleleMapper original allele to haplotype map * @param alleleMapper original allele to haplotype map
*/ */
private VariantContext removeAltAllelesIfTooManyGenotypes(final int ploidy, final Map<Allele, List<Haplotype>> alleleMapper, final VariantContext mergedVC) { private synchronized VariantContext removeAltAllelesIfTooManyGenotypes(final int ploidy, final Map<Allele, List<Haplotype>> alleleMapper, final VariantContext mergedVC) {
final int originalAlleleCount = alleleMapper.size(); final int originalAlleleCount = alleleMapper.size();
practicalAlleleCountForPloidy.putIfAbsent(ploidy, GenotypeLikelihoodCalculators.computeMaxAcceptableAlleleCount(ploidy, maxGenotypeCountToEnumerate)); practicalAlleleCountForPloidy.putIfAbsent(ploidy, GenotypeLikelihoodCalculators.computeMaxAcceptableAlleleCount(ploidy, maxGenotypeCountToEnumerate));