From 7dc6f733995760369fd6693b20328728ebb4e3f1 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 14 Feb 2012 21:11:24 -0500 Subject: [PATCH] Bug fix for validation site selector: records with AC=0 in them were always being thrown out if input vcf was sites-only, even when -ignorePolymorphicStatus flag was set --- .../UniformSamplingFrequencySelector.java | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java index 66720a252..eda75d647 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java @@ -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