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Thanks to Menachem for pointing out that the docs for genotyping_mode and output_mode were the same (and unclear). Fixed.

This commit is contained in:
Eric Banks 2012-04-19 12:48:09 -04:00
parent 2485cef5b8
commit 79272c5e15
1 changed files with 2 additions and 5 deletions
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7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -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;
/**