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Mark several indel-related arguments as @Hidden

This commit is contained in:
Guillermo del Angel 2011-07-06 09:56:38 -04:00
parent 5298e3a942
commit 81a4d18468
1 changed files with 7 additions and 1 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -92,25 +92,31 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false)
public double INDEL_HETEROZYGOSITY = 1.0/8000;
@Hidden
@Argument(fullName = "indelGapContinuationPenalty", shortName = "indelGCP", doc = "Indel gap continuation penalty", required = false)
public double INDEL_GAP_CONTINUATION_PENALTY = 10.0;
@Hidden
@Argument(fullName = "indelGapOpenPenalty", shortName = "indelGOP", doc = "Indel gap open penalty", required = false)
public double INDEL_GAP_OPEN_PENALTY = 45.0;
@Hidden
@Argument(fullName = "indelHaplotypeSize", shortName = "indelHSize", doc = "Indel haplotype size", required = false)
public int INDEL_HAPLOTYPE_SIZE = 80;
@Hidden
@Argument(fullName = "doContextDependentGapPenalties", shortName = "doCDP", doc = "Vary gap penalties by context", required = false)
public boolean DO_CONTEXT_DEPENDENT_PENALTIES = true;
//gdebug+
@Hidden
// experimental arguments, NOT TO BE USED BY ANYONE WHOSE INITIALS AREN'T GDA!!!
@Hidden
@Argument(fullName = "getGapPenaltiesFromData", shortName = "dataGP", doc = "Vary gap penalties by context - EXPERIMENTAL, DO NO USE", required = false)
public boolean GET_GAP_PENALTIES_FROM_DATA = false;
@Hidden
@Argument(fullName="indel_recal_file", shortName="recalFile", required=false, doc="Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE")
public File INDEL_RECAL_FILE = new File("indel.recal_data.csv");
@Hidden
@Argument(fullName = "indelDebug", shortName = "indelDebug", doc = "Output indel debug info", required = false)
public boolean OUTPUT_DEBUG_INDEL_INFO = false;
@Hidden