From 0b43ee117cd06a138309a3d18be3b3809be87c9f Mon Sep 17 00:00:00 2001 From: Kiran V Garimella Date: Mon, 25 Jul 2011 11:35:34 -0400 Subject: [PATCH] Added the required=false tag to the -noST and -noEV arguments so the auto-help output doesn't look weird (i.e. listing arguments as required when their value has already been specified by default). --- .../sting/gatk/walkers/varianteval/VariantEvalWalker.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index fe3173506..3867aa958 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -67,7 +67,7 @@ public class VariantEvalWalker extends RodWalker implements Tr @Argument(fullName="stratificationModule", shortName="ST", doc="One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)", required=false) protected String[] STRATIFICATIONS_TO_USE = {}; - @Argument(fullName="doNotUseAllStandardStratifications", shortName="noST", doc="Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)") + @Argument(fullName="doNotUseAllStandardStratifications", shortName="noST", doc="Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)", required=false) protected Boolean NO_STANDARD_STRATIFICATIONS = false; @Argument(fullName="onlyVariantsOfType", shortName="VT", doc="If provided, only variants of these types will be considered during the evaluation, in ", required=false) @@ -77,7 +77,7 @@ public class VariantEvalWalker extends RodWalker implements Tr @Argument(fullName="evalModule", shortName="EV", doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)", required=false) protected String[] MODULES_TO_USE = {}; - @Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)") + @Argument(fullName="doNotUseAllStandardModules", shortName="noEV", doc="Do not use the standard modules by default (instead, only those that are specified with the -E option)", required=false) protected Boolean NO_STANDARD_MODULES = false; // Other arguments