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GenotypeAndValidate - Added docs to the @Arguments

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Mauricio Carneiro 2011-08-19 13:34:21 -04:00
parent a97639b343
commit 7b5fa4486d
1 changed files with 29 additions and 4 deletions
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33
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
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@ -25,10 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.validation;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -201,30 +198,58 @@ import static org.broadinstitute.sting.utils.IndelUtils.isInsideExtendedIndel;
public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalker.CountedData, GenotypeAndValidateWalker.CountedData> implements TreeReducible<GenotypeAndValidateWalker.CountedData> {
/**
* The optional output file that will have all the variants used in the Genotype and Validation essay.
*/
@Output(doc="Generate a VCF file with the variants considered by the walker, with a new annotation \"callStatus\" which will carry the value called in the validation VCF or BAM file", required=false)
protected VCFWriter vcfWriter = null;
/**
* The callset to be used as truth (default) or validated (if BAM file is set to truth).
*/
@Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype", required=true)
public RodBinding<VariantContext> alleles;
/**
* Makes the Unified Genotyper calls to the BAM file the truth dataset and validates the alleles ROD binding callset.
*/
@Argument(fullName ="set_bam_truth", shortName ="bt", doc="Use the calls on the reads (bam file) as the truth dataset and validate the calls on the VCF", required=false)
private boolean bamIsTruth = false;
/**
* The minimum base quality score necessary for a base to be considered when calling a genotype. This argument is passed to the Unified Genotyper.
*/
@Argument(fullName="minimum_base_quality_score", shortName="mbq", doc="Minimum base quality score for calling a genotype", required=false)
private int mbq = -1;
/**
* The maximum deletion fraction allowed in a site for calling a genotype. This argument is passed to the Unified Genotyper.
*/
@Argument(fullName="maximum_deletion_fraction", shortName="deletions", doc="Maximum deletion fraction for calling a genotype", required=false)
private double deletions = -1;
/**
* the minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. This argument is passed to the Unified Genotyper.
*/
@Argument(fullName="standard_min_confidence_threshold_for_calling", shortName="stand_call_conf", doc="the minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls", required=false)
private double callConf = -1;
/**
* the minimum phred-scaled Qscore threshold to emit low confidence calls. This argument is passed to the Unified Genotyper.
*/
@Argument(fullName="standard_min_confidence_threshold_for_emitting", shortName="stand_emit_conf", doc="the minimum phred-scaled Qscore threshold to emit low confidence calls", required=false)
private double emitConf = -1;
/**
* Only validate sites that have at least a given depth
*/
@Argument(fullName="condition_on_depth", shortName="depth", doc="Condition validation on a minimum depth of coverage by the reads", required=false)
private int minDepth = -1;
/**
* If your VCF or BAM file has more than one sample and you only want to validate one, use this parameter to choose it.
*/
@Hidden
@Argument(fullName ="sample", shortName ="sn", doc="Name of the sample to validate (in case your VCF/BAM has more than one sample)", required=false)
private String sample = "";