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Bug fixes and rewrite of logic of several parts in SelectVariants: 

a) If we were selecting SNPs or Indels and there was one of each at the same location, only whichever one was pulled first was processed.
b) Fixed logic error when selecting Mendelian Violations: if that option was used it wasn't possible to combine with other options.
c) Fixed logic error when using -disc option: you shouldn't parse genotypes to check whether a site is present or not because a vcf can be sites-only and this is slow.
d) Made -disc option work in the same way as other options: variants are now selected from "variant" track all the time, and variants which are not in disc track are kept. Inverse logic (keep disc variants not present in "variant") is confusing and prevents users from combining with different options.

With these changes it is now possible to ask for example "Give me all indels which are Mendelian Violations, not in dbsnp and present in these samples" which was not possible before.

Integration tests covering the above are forthcoming.

 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6027 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-06-22 14:05:00 +00:00
parent 9b54239f37
commit b7a1beff3c
1 changed files with 37 additions and 53 deletions
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90
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -68,6 +68,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="excludeFiltered", shortName="ef", doc="Don't include filtered loci.", required=false)
private boolean EXCLUDE_FILTERED = false;
@Argument(fullName="discordance", shortName = "disc", doc="Output variants that were not called on a ROD comparison track. Use -disc ROD_NAME", required=false)
private String discordanceRodName = "";
@ -209,68 +210,51 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
Collection<VariantContext> vcs = tracker.getVariantContexts(ref, variantRodName, null, context.getLocation(), true, false);
// If a discordance rod name was provided, we select the variants present in the discordance that
// are not present in the variant.
if (DISCORDANCE_ONLY) {
if (vcs == null || vcs.size() == 0) {
VariantContext compVC = tracker.getVariantContext(ref, discordanceRodName, context.getLocation());
if (compVC != null) {
// if the genotype of any of the samples we're looking it is HET or HomVar, we write this variant
for (String sample : samples) {
Genotype g = compVC.getGenotype(sample);
if ( g != null && (g.isHet() || g.isHomVar()) ) {
vcfWriter.add(compVC, ref.getBase());
return 1;
}
}
}
}
}
if ( vcs == null || vcs.size() == 0) {
return 0;
}
for (VariantContext vc : vcs) {
if (MENDELIAN_VIOLATIONS) {
if (mv.isViolation(vc)) {
vcfWriter.add(vc, ref.getBase());
if (!mv.isViolation(vc)) {
break;
}
}
if (DISCORDANCE_ONLY) {
Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, discordanceRodName, null, context.getLocation(), true, false);
if (!compVCs.isEmpty())
return 0; // return is correct: no matter what vcs has, if compVC is not empty there's nothing more to do at this site
}
if (CONCORDANCE_ONLY) {
Collection<VariantContext> compVCs = tracker.getVariantContexts(ref, concordanceRodName, null, context.getLocation(), true, false);
if (compVCs.isEmpty())
return 0; // return is correct: no matter what vcs has, if compVC is empty there's nothing more to do at this site
}
// TODO - add ability to also select MNPs
// TODO - move variant selection arguments to the engine so other walkers can also do this
if (SELECT_INDELS && !(vc.isIndel() || vc.isMixed()))
continue;
if (SELECT_SNPS && !vc.isSNP())
continue;
VariantContext sub = subsetRecord(vc, samples);
if ( (sub.isPolymorphic() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) {
//System.out.printf("%s%n",sub.toString());
for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) {
if ( !VariantContextUtils.match(sub, jexl) ) {
return 0;
}
}
if (SELECT_RANDOM_NUMBER) {
randomlyAddVariant(++variantNumber, sub, ref.getBase());
}
else if (!SELECT_RANDOM_FRACTION || GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom) {
vcfWriter.add(sub, ref.getBase());
}
}
else if (CONCORDANCE_ONLY) {
VariantContext compVC = tracker.getVariantContext(ref, concordanceRodName, context.getLocation());
if (compVC != null) {
vcfWriter.add(vc, ref.getBase());
break; // we only want one line per event in this case.
}
}
else {
// TODO - add ability to also select MNPs
// TODO - move variant selection arguments to the engine so other walkers can also do this
if (SELECT_INDELS && vc.isSNP())
return 0;
if (SELECT_SNPS && (vc.isIndel() || vc.isMixed()))
return 0;
VariantContext sub = subsetRecord(vc, samples);
if ( (sub.isPolymorphic() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) {
//System.out.printf("%s%n",sub.toString());
for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) {
if ( !VariantContextUtils.match(sub, jexl) ) {
return 0;
}
}
if (SELECT_RANDOM_NUMBER) {
randomlyAddVariant(++variantNumber, sub, ref.getBase());
}
else if (!SELECT_RANDOM_FRACTION || GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom) {
vcfWriter.add(sub, ref.getBase());
}
}
}
}
return 1;