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Updating SelectVariants documentation to reflect best practice

This commit is contained in:
Mark DePristo 2011-08-10 22:24:18 -04:00
parent b984b7aa9b
commit cb6cf25bb0
1 changed files with 0 additions and 10 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -54,17 +54,9 @@ import java.util.*;
* recompute the value of certain annotations based on the new sample set, and output a new VCF with the results. * recompute the value of certain annotations based on the new sample set, and output a new VCF with the results.
*/ */
public class SelectVariants extends RodWalker<Integer, Integer> { public class SelectVariants extends RodWalker<Integer, Integer> {
/**
* The VCF file we are selecting variants from.
*
* Variants from this file are sent through the filtering and modifying routines as directed
* by the arguments to SelectVariants, and finally are emitted.
*/
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
/** /**
* If provided, we will filter out variants that are "discordant" to the variants in this file
*
* A site is considered discordant if there exists some sample in eval that has a non-reference genotype * A site is considered discordant if there exists some sample in eval that has a non-reference genotype
* and either the site isn't present in this track, the sample isn't present in this track, * and either the site isn't present in this track, the sample isn't present in this track,
* or the sample is called reference in this track. * or the sample is called reference in this track.
@ -73,8 +65,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
private RodBinding<VariantContext> discordanceTrack = RodBinding.makeUnbound(VariantContext.class); private RodBinding<VariantContext> discordanceTrack = RodBinding.makeUnbound(VariantContext.class);
/** /**
* If provided, we will filter out any variant in variants that isn't "concordant" with the variants in this track.
*
* A site is considered concordant if (1) we are not looking for specific samples and there is a variant called * A site is considered concordant if (1) we are not looking for specific samples and there is a variant called
* in both variants and concordance tracks or (2) every sample present in eval is present in the concordance * in both variants and concordance tracks or (2) every sample present in eval is present in the concordance
* track and they have the sample genotype call. * track and they have the sample genotype call.