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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
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kiran 2010-08-08 04:12:01 +00:00
parent eb1bb94d1c
commit 0da0dfa1da
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -29,16 +29,16 @@ import java.util.regex.Pattern;
*/
@Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
public class SelectVariants extends RodWalker<Integer, Integer> {
@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<String> 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<String> SELECT_EXPRESSIONS = new ArrayList<String>();
@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<String> selectNames = new ArrayList<String>();