From 2748eb60e14503a2f7e9cea739c35b718d01ebf9 Mon Sep 17 00:00:00 2001 From: kiran Date: Sat, 12 Dec 2009 21:41:07 +0000 Subject: [PATCH] Added short documentation for each class so that it appears in the walker command-line documentation. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2340 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/filters/VariantFiltrationWalker.java | 2 +- .../contamination/FindContaminatingReadGroupsWalker.java | 9 ++------- .../gatk/walkers/variantstovcf/VariantsToVCF.java | 3 +++ .../gatk/walkers/vcftools/VCFSubsetWalker.java | 3 +++ 4 files changed, 9 insertions(+), 8 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 2391d99ab..183298e47 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -13,7 +13,7 @@ import org.apache.commons.jexl.*; /** - * VariantFiltrationWalker filters variant calls in VCF format. + * Filters variant calls using a number of user-selectable, parameterizable criteria. */ @Requires(value={},referenceMetaData=@RMD(name="variant",type= RodVCF.class)) public class VariantFiltrationWalker extends RodWalker { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java index bd91a8a22..d6e0c884f 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java @@ -24,13 +24,8 @@ import cern.jet.stat.Probability; /** * FindContaminatingReadGroupsWalker lists read groups in a single-sample BAM file that appear - * to be contaminants by searching for evidence of systematic underperformance at likely - * homozygous-variant sites. First, sites that are likely homozygous-variant but are called - * as heterozygous are identified. Next, per each site and read group, we compute the proportion - * of bases in the pileup supporting an alternate allele. Finally, a one-sample, left-tailed - * t-test is performed with the null hypothesis being that the alternate allele distribution has - * a mean of 0.95 and the alternate hypothesis being that the true mean is statistically - * significantly less than expected. + * to be contaminants (i.e. a read group that's not actually associated with the sample) by searching + * for evidence of systematic underperformance at likely homozygous-variant sites. * * @author Kiran Garimella */ diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java index 84bc2e1e8..bc2323720 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java @@ -20,6 +20,9 @@ import java.io.File; import java.io.PrintStream; import java.util.*; +/** + * Converts variants from other file formats (anything that implements the Variation interface) to VCF format. + */ public class VariantsToVCF extends RefWalker { @Argument(fullName="vcfout", shortName="VO", doc="The output VCF file") public File VCF_OUT; @Argument(fullName="verbose", shortName="V", doc="Show extended output", required=false) public boolean VERBOSE = false; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java index f42dc83d1..8cc8e403f 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java @@ -12,6 +12,9 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import java.util.*; import java.io.File; +/** + * Extracts subsets of a VCF file like one or more samples, all or only variant loci, all or filtered loci. + */ public class VCFSubsetWalker extends RefWalker, VCFWriter> { @Argument(fullName="sample", shortName="SN", doc="Sample to include (or nothing to specify all samples)", required=false) private HashSet SAMPLES;