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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-02-18 10:55:29 -05:00
parent a8be96f63d e724c63f2b
commit 3d9eee4942
1 changed files with 9 additions and 6 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
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@ -52,13 +52,16 @@ public class UniformSamplingFrequencySelector extends FrequencyModeSelector {
if (! selectedInTargetSamples && !IGNORE_POLYMORPHIC)
return;
} else {
if ( attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY) ) {
int ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
if (ac == 0) return; // site not polymorphic
if (!IGNORE_POLYMORPHIC) {
if (vc.getAttributes().containsKey(VCFConstants.ALLELE_COUNT_KEY))
{
int ac = vc.getAttributeAsInt(VCFConstants.ALLELE_COUNT_KEY, 0);
if (ac == 0) return; // site not polymorphic
}
else
// no allele count field in VC
return;
}
else
return;
}
// create bare-bones event and log in corresponding bin
// attributes contains AC,AF,AN pulled from original vc, and we keep them here and log in output file for bookkeeping purposes