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Fix descriptions of walker args 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1436 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-18 19:46:48 +00:00
parent 82e2b7017e
commit b3fe566c0c
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyper.java
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@ -26,14 +26,14 @@ public class SingleSampleGenotyper extends LocusWalker<SSGGenotypeCall, Genotype
@Argument(fullName = "variants_out", shortName = "varout", doc = "File to which variants should be written", required = false)
public File VARIANTS_FILE = null;
@Argument(fullName = "variant_output_format", shortName = "vf", doc = "File to which metrics should be written", required = false)
@Argument(fullName = "variant_output_format", shortName = "vf", doc = "File format to be used", required = false)
public GenotypeWriterFactory.GENOTYPE_FORMAT VAR_FORMAT = GenotypeWriterFactory.GENOTYPE_FORMAT.GELI;
// Control what goes into the variants file and what format that file should have
@Argument(fullName = "lod_threshold", shortName = "lod", doc = "The lod threshold on which variants should be filtered", required = false)
public Double LOD_THRESHOLD = Double.MIN_VALUE;
@Argument(fullName = "genotype", shortName = "genotype", doc = "Should we output confidient genotypes or just the variants?", required = false)
@Argument(fullName = "genotype", shortName = "genotype", doc = "Should we output confident genotypes or just the variants?", required = false)
public boolean GENOTYPE = false;
// Control how the genotype hypotheses are weighed