From 26e71f6688781b4f4de4c9e13269b64f0409d13d Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 27 Sep 2011 11:03:17 -0400 Subject: [PATCH] The Omni files have multiple records (with the same ALT) at a particular location, with one PASSing and the other(s) filtered. Chris, this is why using this file as both eval and comp leads to ref/no-call cells in the GenotypeConcordance table. However, this led to non-determinism in VE because the VCs were placed in a HashSet; we use a LinkedHashMap instead to bring back determinism. --- .../sting/gatk/walkers/varianteval/util/VariantEvalUtils.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java index 92e7c6554..6a057a456 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java @@ -354,7 +354,7 @@ public class VariantEvalUtils { private void addMapping(HashMap> mappings, String sample, VariantContext vc) { if ( !mappings.containsKey(sample) ) - mappings.put(sample, new HashSet()); + mappings.put(sample, new LinkedHashSet()); mappings.get(sample).add(vc); }