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update to deal with partial indels (I/D with no bases) in the HM records 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3820 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-07-18 02:56:37 +00:00
parent 25a27b78bc
commit 982947d328
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -520,7 +520,7 @@ public class VariantContextAdaptors {
Map<String, Genotype> genotypes = new HashMap<String, Genotype>(samples.length);
for ( int i = 0; i < samples.length; i++ ) {
// ignore bad genotypes
if ( genotypeStrings[i].contains("N") )
if ( genotypeStrings[i].contains("N") || genotypeStrings[i].contains("I") || genotypeStrings[i].contains("D") )
continue;
String a1 = genotypeStrings[i].substring(0,1);