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Two new arguments to SelectVariants to exclude either multiallelic or biallelic sites from input vcf

This commit is contained in:
Guillermo del Angel 2011-08-23 12:40:01 -04:00
parent bcc0cae89e
commit 8b7a0b3b62
1 changed files with 12 additions and 0 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -223,6 +223,12 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="excludeFiltered", shortName="ef", doc="Don't include filtered loci in the analysis", required=false) @Argument(fullName="excludeFiltered", shortName="ef", doc="Don't include filtered loci in the analysis", required=false)
private boolean EXCLUDE_FILTERED = false; private boolean EXCLUDE_FILTERED = false;
@Argument(fullName="excludeBiallelic", shortName="xl_biallelic", doc="Select only multi-allelic variants, excluding any biallelic one.", required=false)
private boolean EXCLUDE_BIALLELIC = false;
@Argument(fullName="selectMultiallelic", shortName="xl_multiallelic", doc="Select only biallelic variants, excluding any multi-allelic one.", required=false)
private boolean EXCLUDE_MULTIALLELIC = false;
@Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't update the AC, AF, or AN values in the INFO field after selecting", required=false) @Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't update the AC, AF, or AN values in the INFO field after selecting", required=false)
private boolean KEEP_ORIGINAL_CHR_COUNTS = false; private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
@ -335,6 +341,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
// first, add any requested samples // first, add any requested samples
samples.addAll(samplesFromFile); samples.addAll(samplesFromFile);
samples.addAll(samplesFromExpressions); samples.addAll(samplesFromExpressions);
if (sampleNames != null)
samples.addAll(sampleNames); samples.addAll(sampleNames);
// if none were requested, we want all of them // if none were requested, we want all of them
@ -493,6 +500,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
if (!isConcordant(vc, compVCs)) if (!isConcordant(vc, compVCs))
return 0; return 0;
} }
if (EXCLUDE_BIALLELIC && vc.isBiallelic())
return 0;
if (EXCLUDE_MULTIALLELIC && !vc.isBiallelic())
return 0;
// TODO - add ability to also select MNPs // TODO - add ability to also select MNPs
// TODO - move variant selection arguments to the engine so other walkers can also do this // TODO - move variant selection arguments to the engine so other walkers can also do this