From 79272c5e1523f1fd11fca1cce7f8617890cde3d3 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 19 Apr 2012 12:48:09 -0400 Subject: [PATCH] Thanks to Menachem for pointing out that the docs for genotyping_mode and output_mode were the same (and unclear). Fixed. --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index d7174536e..f4ffbad91 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -55,13 +55,10 @@ public class UnifiedArgumentCollection { @Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false) public Double PCR_error = DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.DEFAULT_PCR_ERROR_RATE; - /** - * Specifies how to determine the alternate allele to use for genotyping - */ - @Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Should we output confident genotypes (i.e. including ref calls) or just the variants?", required = false) + @Argument(fullName = "genotyping_mode", shortName = "gt_mode", doc = "Specifies how to determine the alternate alleles to use for genotyping", required = false) public GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; - @Argument(fullName = "output_mode", shortName = "out_mode", doc = "Should we output confident genotypes (i.e. including ref calls) or just the variants?", required = false) + @Argument(fullName = "output_mode", shortName = "out_mode", doc = "Specifies which type of calls we should output", required = false) public UnifiedGenotyperEngine.OUTPUT_MODE OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; /**