zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Continue to fix the case where PRIORITIZE is used but no priority list is given. While fixing that case I also removed unnecessary sorting, when the prioeity list is not provied. When the priority list is not provided, it will continue to be null. Thus, the number of original Variant Contexts should be given as a new parameter to simpleMerge (since priority might be null). This new parameter is used for checking if there are filtered VC, when annotationOrigin is true.

This commit is contained in:
Ami Levy-Moonshine 2012-12-10 22:23:58 -05:00
parent 573ace4403
commit 2e3284f306
2 changed files with 43 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -228,7 +228,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> 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<String>(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<Integer, Integer> implements Tree
if ( tracker == null ) // RodWalkers can make funky map calls
return 0;
Set<String> 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<VariantContext> vcs = tracker.getValues(variants, context.getLocation());
@ -289,13 +290,13 @@ public class CombineVariants extends RodWalker<Integer, Integer> 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 {

42
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -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<VariantContext> unsortedVCs,
final List<String> 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;