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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.

This commit is contained in:
Eric Banks 2011-09-27 11:03:17 -04:00
parent e99ff3caae
commit 26e71f6688
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
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@ -354,7 +354,7 @@ public class VariantEvalUtils {
private void addMapping(HashMap<String, Set<VariantContext>> mappings, String sample, VariantContext vc) { private void addMapping(HashMap<String, Set<VariantContext>> mappings, String sample, VariantContext vc) {
if ( !mappings.containsKey(sample) ) if ( !mappings.containsKey(sample) )
mappings.put(sample, new HashSet<VariantContext>()); mappings.put(sample, new LinkedHashSet<VariantContext>());
mappings.get(sample).add(vc); mappings.get(sample).add(vc);
} }