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Added missing javadoc info to Beagle arguments

This commit is contained in:
Guillermo del Angel 2011-09-07 13:21:11 -04:00
parent d5641cfac5
commit 5f22ef9a8c
2 changed files with 24 additions and 0 deletions
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21
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -79,24 +79,45 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
/**
* If this argument is present, the original allele frequencies and counts from this vcf are added as annotations ACH,AFH and ANH. at each record present in this vcf
*/
@Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
public RodBinding<VariantContext> comp;
/**
* This required argument is used to annotate each site in the vcf INFO field with R2 annotation. Will be NaN if Beagle determined there are no variant samples.
*/
@Input(fullName="beagleR2", shortName = "beagleR2", doc="Beagle-produced .r2 file containing R^2 values for all markers", required=true)
public RodBinding<BeagleFeature> beagleR2;
/**
* These values will populate the GL field for each sample and contain the posterior probability of each genotype given the data after phasing and imputation.
*/
@Input(fullName="beagleProbs", shortName = "beagleProbs", doc="Beagle-produced .probs file containing posterior genotype probabilities", required=true)
public RodBinding<BeagleFeature> beagleProbs;
/**
* By default, all genotypes will be marked in the VCF as "phased", using the "|" separator after Beagle.
*/
@Input(fullName="beaglePhased", shortName = "beaglePhased", doc="Beagle-produced .phased file containing phased genotypes", required=true)
public RodBinding<BeagleFeature> beaglePhased;
@Output(doc="VCF File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;
/**
* If this argument is absent, and if Beagle determines that there is no sample in a site that has a variant genotype, the site will be marked as filtered (Default behavior).
* If the argument is present, the site won't be marked as filtered under this condition even if there are no variant genotypes.
*/
@Argument(fullName="dont_mark_monomorphic_sites_as_filtered", shortName="keep_monomorphic", doc="If provided, we won't filter sites that beagle tags as monomorphic. Useful for imputing a sample's genotypes from a reference panel" ,required=false)
public boolean DONT_FILTER_MONOMORPHIC_SITES = false;
/**
* Value between 0 and 1. If the probability of getting a genotype correctly (based on the posterior genotype probabilities and the actual genotype) is below this threshold,
* a genotype will be substitute by a no-call.
*/
@Argument(fullName="no" +
"call_threshold", shortName="ncthr", doc="Threshold of confidence at which a genotype won't be called", required=false)
private double noCallThreshold = 0.0;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
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@ -112,6 +112,9 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
@Argument(fullName = "bootstrap_vcf",shortName = "bvcf", doc = "Output a VCF with the records used for bootstrapping filtered out", required = false)
VCFWriter bootstrapVCFOutput = null;
/**
* If sample gender is known, this flag should be set to true to ensure that Beagle treats male Chr X properly.
*/
@Argument(fullName = "checkIsMaleOnChrX", shortName = "checkIsMaleOnChrX", doc = "Set to true when Beagle-ing chrX and want to ensure male samples don't have heterozygous calls.", required = false)
public boolean CHECK_IS_MALE_ON_CHR_X = false;