From 0ecb85d3212459e959a9d28ad979e977579cfd89 Mon Sep 17 00:00:00 2001 From: Laura Gauthier Date: Tue, 3 Jun 2014 14:41:32 -0400 Subject: [PATCH] Added docs to VariantFiltration is accordance with new htsjdk changes. Fixed typo in VariantAnnotator docs. --- .../gatk/tools/walkers/annotator/VariantAnnotator.java | 2 +- .../gatk/tools/walkers/filters/VariantFiltration.java | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java index ed0d39761..042ba487f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotator.java @@ -135,7 +135,7 @@ public class VariantAnnotator extends RodWalker implements Ann protected VariantContextWriter vcfWriter = null; /** - * See the -list argument to view available annotations. + * See the --list argument to view available annotations. */ @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false) protected List annotationsToUse = new ArrayList<>(); diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java index 7d833405b..3988498c0 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltration.java @@ -115,7 +115,8 @@ public class VariantFiltration extends RodWalker { * Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead. * VariantFiltration will add the sample-level FT tag to the FORMAT field of filtered samples (this does not affect the record's FILTER tag). * One can filter normally based on most fields (e.g. "GQ < 5.0"), but the GT (genotype) field is an exception. We have put in convenience - * methods so that one can now filter out hets ("isHet == 1"), refs ("isHomRef == 1"), or homs ("isHomVar == 1"). + * methods so that one can now filter out hets ("isHet == 1"), refs ("isHomRef == 1"), or homs ("isHomVar == 1"). Also available are + * expressions isCalled, isNoCall, isMixed, and isAvailable, in accordance with the methods of the Genotype object. */ @Argument(fullName="genotypeFilterExpression", shortName="G_filter", doc="One or more expression used with FORMAT (sample/genotype-level) fields to filter (see documentation guide for more info)", required=false) protected ArrayList GENOTYPE_FILTER_EXPS = new ArrayList();