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Set ROD priority list to input

This commit is contained in:
Joel Thibault 2012-04-20 14:51:21 -04:00
parent a7fe847faf
commit 1cda87a4ad
1 changed files with 2 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -673,7 +673,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
//defaults from CombineVariants //defaults from CombineVariants
VariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = VariantContextUtils.MultipleAllelesMergeType.BY_TYPE; VariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = VariantContextUtils.MultipleAllelesMergeType.BY_TYPE;
List<String> priority = new ArrayList<String>(VCFUtils.getVCFHeadersFromRods(getToolkit()).keySet()); List<String> priority = new ArrayList<String>();
priority.add("input");
VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED; VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED;
VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE; VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE;
boolean printComplexMerges = false; boolean printComplexMerges = false;