From 0da0dfa1da28747a702f4d6a13f27640f634e935 Mon Sep 17 00:00:00 2001 From: kiran Date: Sun, 8 Aug 2010 04:12:01 +0000 Subject: [PATCH] Cosmetic change - lower-case for all command-line arguments' short names. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3971 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/variantutils/SelectVariants.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 0c63eb752..1173f6cef 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -29,16 +29,16 @@ import java.util.regex.Pattern; */ @Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class)) public class SelectVariants extends RodWalker { - @Argument(fullName="sample", shortName="SN", doc="Sample(s) to include. Can be a single sample, specified multiple times for many samples, or a regular expression to select many samples.", required=false) + @Argument(fullName="sample", shortName="sn", doc="Sample(s) to include. Can be a single sample, specified multiple times for many samples, or a regular expression to select many samples.", required=false) public Set SAMPLE_EXPRESSIONS; @Argument(shortName="select", doc="One or more criteria to use when selecting the data. Evaluated *after* the specified samples are extracted and the INFO-field annotations are updated.", required=false) public ArrayList SELECT_EXPRESSIONS = new ArrayList(); - @Argument(fullName="excludeNonVariants", shortName="ENV", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false) + @Argument(fullName="excludeNonVariants", shortName="env", doc="Don't include loci found to be non-variant after the subsetting procedure.", required=false) private boolean EXCLUDE_NON_VARIANTS = false; - @Argument(fullName="excludeFiltered", shortName="EF", doc="Don't include filtered loci.", required=false) + @Argument(fullName="excludeFiltered", shortName="ef", doc="Don't include filtered loci.", required=false) private boolean EXCLUDE_FILTERED = false; private ArrayList selectNames = new ArrayList();