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Merge pull request #764 from broadinstitute/ldg_fixCombineVariantsError 

Minor change to new CombineVariants error check so identical samples don...
This commit is contained in:
rpoplin 2014-10-31 15:23:23 -04:00
parent 2d7f906a27 7bae70ec1a
commit 2ff88d17ca
1 changed files with 1 additions and 1 deletions
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public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
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@ -211,7 +211,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
final boolean sampleNamesAreUnique = SampleUtils.verifyUniqueSamplesNames(vcfRods);
if (genotypeMergeOption == null) {
if (genotypeMergeOption == null && !ASSUME_IDENTICAL_SAMPLES) {
if (!sampleNamesAreUnique)
throw new UserException("Duplicate sample names were discovered but no genotypemergeoption was supplied. " +
"To combine samples without merging specify --genotypemergeoption UNIQUIFY. Merging duplicate samples " +