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indelGOP and indelGCP are now advanced, not hidden arguments

This commit is contained in:
Mark DePristo 2012-08-06 11:42:36 -04:00
parent 2f004665fb
commit 44f160f29f
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -146,12 +146,12 @@ 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)
@Advanced
@Argument(fullName = "indelGapContinuationPenalty", shortName = "indelGCP", doc = "Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10", required = false)
public byte INDEL_GAP_CONTINUATION_PENALTY = 10;
@Hidden
@Argument(fullName = "indelGapOpenPenalty", shortName = "indelGOP", doc = "Indel gap open penalty", required = false)
@Advanced
@Argument(fullName = "indelGapOpenPenalty", shortName = "indelGOP", doc = "Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10", required = false)
public byte INDEL_GAP_OPEN_PENALTY = 45;
@Hidden