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Add simple ability to create "X out of N" combined files: if a site is present in at least X input rods, it gets output, otherwise it's skipped, controlled with argument -minN. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5783 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-05-10 15:27:18 +00:00
parent f275be6968
commit 3c364279f4
1 changed files with 14 additions and 1 deletions
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15
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -83,6 +83,9 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="assumeIdenticalSamples", shortName="assumeIdenticalSamples", doc="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime.", required=false)
public boolean ASSUME_IDENTICAL_SAMPLES = false;
@Argument(fullName="minimumN", shortName="minN", doc="Combine variants and output site only if variant is present in at least N input files.", required=false)
public int minimumN = 1;
@Hidden
@Argument(fullName="mergeInfoWithMaxAC", shortName="mergeInfoWithMaxAC", doc="If true, when VCF records overlap the info field is taken from the one with the max AC instead of only taking the fields which are identical across the overlapping records.", required=false)
public boolean MERGE_INFO_WITH_MAX_AC = false;
@ -133,7 +136,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
// get all of the vcf rods at this locus
// Need to provide reference bases to simpleMerge starting at current locus
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, null,context.getLocation(), true, false);
if ( ASSUME_IDENTICAL_SAMPLES ) {
for ( final VariantContext vc : vcs ) {
@ -143,6 +146,16 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
return vcs.isEmpty() ? 0 : 1;
}
int numFilteredRecords = 0;
for (VariantContext vc : vcs) {
if (vc.filtersWereApplied() && vc.isFiltered())
numFilteredRecords++;
}
if (vcs.size() - numFilteredRecords < minimumN)
return 0;
VariantContext mergedVC = null;
if ( variantMergeOption == VariantContextUtils.VariantMergeType.MASTER ) {
mergedVC = VariantContextUtils.masterMerge(vcs, "master");