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SelectVariants fully documented, now the shining example of the new RodBinding system.

This commit is contained in:
Mark DePristo 2011-08-04 18:28:59 -04:00
parent 9308fbe3fb
commit f21f7f6335
1 changed files with 27 additions and 7 deletions
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34
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -55,9 +55,35 @@ import java.util.*;
*/
@Requires(value={})
public class SelectVariants extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
/**
* 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.
*/
@Input(fullName="variants", shortName = "V", doc="Select variants from this VCF file", required=true)
public RodBinding<VariantContext> variants;
/**
* 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
* 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.
*/
@Input(fullName="discordance", shortName = "disc", doc="Output variants that were not called in this Feature comparison track", required=false)
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
* 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.
*/
@Input(fullName="concordance", shortName = "conc", doc="Output variants that were also called in this Feature comparison track", required=false)
private RodBinding<VariantContext> concordanceTrack = RodBinding.makeUnbound(VariantContext.class);
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;
@ -82,12 +108,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't include filtered loci.", required=false)
private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
@Argument(fullName="discordance", shortName = "disc", doc="Output variants that were not called on a ROD comparison track", required=false)
private RodBinding<VariantContext> discordanceTrack = RodBinding.makeUnbound(VariantContext.class);
@Argument(fullName="concordance", shortName = "conc", doc="Output variants that were also called on a ROD comparison track", required=false)
private RodBinding<VariantContext> concordanceTrack = RodBinding.makeUnbound(VariantContext.class);
@Hidden
@Argument(fullName="keepAFSpectrum", shortName="keepAF", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false)
private boolean KEEP_AF_SPECTRUM = false;