diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java index 1d4913769..68fac7631 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java @@ -228,7 +228,7 @@ public class CombineVariants extends RodWalker implements Tree if ( genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE && PRIORITY_STRING == null ) throw new UserException.MissingArgument("rod_priority_list", "Priority string must be provided if you want to prioritize genotypes"); - if ( PRIORITY_STRING != null || genotypeMergeOption == VariantContextUtils.GenotypeMergeType.PRIORITIZE ){ + if ( PRIORITY_STRING != null){ priority = new ArrayList(Arrays.asList(PRIORITY_STRING.split(","))); if ( rodNames.size() != priority.size() ) throw new UserException.BadArgumentValue("rod_priority_list", "The priority list must contain exactly one rod binding per ROD provided to the GATK: rodNames=" + rodNames + " priority=" + priority); @@ -243,6 +243,7 @@ public class CombineVariants extends RodWalker implements Tree if ( tracker == null ) // RodWalkers can make funky map calls return 0; + Set rodNames = SampleUtils.getRodNamesWithVCFHeader(getToolkit(), null); // get all of the vcf rods at this locus // Need to provide reference bases to simpleMerge starting at current locus Collection vcs = tracker.getValues(variants, context.getLocation()); @@ -289,13 +290,13 @@ public class CombineVariants extends RodWalker implements Tree for (VariantContext.Type type : VariantContext.Type.values()) { if (VCsByType.containsKey(type)) mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type), - priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges, + priority, rodNames.size() , filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges, SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC)); } } else if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.MIX_TYPES) { mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), vcs, - priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges, + priority, rodNames.size(), filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges, SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC)); } else { diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index b3e3cf8df..8b360eb5e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -448,11 +448,47 @@ public class VariantContextUtils { final String setKey, final boolean filteredAreUncalled, final boolean mergeInfoWithMaxAC ) { + int originalNumOfVCs = priorityListOfVCs == null ? 0 : priorityListOfVCs.size(); + return simpleMerge(genomeLocParser,unsortedVCs,priorityListOfVCs,originalNumOfVCs,filteredRecordMergeType,genotypeMergeOptions,annotateOrigin,printMessages,setKey,filteredAreUncalled,mergeInfoWithMaxAC); + } + + /** + * Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority order, if provided. + * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with + * the sample name + * + * @param genomeLocParser loc parser + * @param unsortedVCs collection of unsorted VCs + * @param priorityListOfVCs priority list detailing the order in which we should grab the VCs + * @param filteredRecordMergeType merge type for filtered records + * @param genotypeMergeOptions merge option for genotypes + * @param annotateOrigin should we annotate the set it came from? + * @param printMessages should we print messages? + * @param setKey the key name of the set + * @param filteredAreUncalled are filtered records uncalled? + * @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count? + * @return new VariantContext representing the merge of unsortedVCs + */ + public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser, + final Collection unsortedVCs, + final List priorityListOfVCs, + final int originalNumOfVCs, + final FilteredRecordMergeType filteredRecordMergeType, + final GenotypeMergeType genotypeMergeOptions, + final boolean annotateOrigin, + final boolean printMessages, + final String setKey, + final boolean filteredAreUncalled, + final boolean mergeInfoWithMaxAC ) { + if ( unsortedVCs == null || unsortedVCs.size() == 0 ) return null; - if ( annotateOrigin && priorityListOfVCs == null ) - throw new IllegalArgumentException("Cannot merge calls and annotate their origins without a complete priority list of VariantContexts"); + if (priorityListOfVCs != null && originalNumOfVCs != priorityListOfVCs.size()) + throw new IllegalArgumentException("the number of the original VariantContexts must be the same as the number of VariantContexts in the priority list"); + + if ( annotateOrigin && priorityListOfVCs == null && originalNumOfVCs == 0) + throw new IllegalArgumentException("Cannot merge calls and annotate their origins without a complete priority list of VariantContexts or the number of original VariantContexts"); if ( genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE ) verifyUniqueSampleNames(unsortedVCs); @@ -597,7 +633,7 @@ public class VariantContextUtils { if ( annotateOrigin ) { // we care about where the call came from String setValue; - if ( nFiltered == 0 && variantSources.size() == priorityListOfVCs.size() ) // nothing was unfiltered + if ( nFiltered == 0 && variantSources.size() == originalNumOfVCs ) // nothing was unfiltered setValue = MERGE_INTERSECTION; else if ( nFiltered == VCs.size() ) // everything was filtered out setValue = MERGE_FILTER_IN_ALL;