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--multiallelic mode is not hidden anymore (but it is annotated as advanced); added docs

This commit is contained in:
Eric Banks 2011-12-20 12:47:38 -05:00
parent 2d619d8633
commit 6f52bd580b
1 changed files with 10 additions and 17 deletions
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27
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -25,10 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -106,6 +103,15 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false)
public Double MAX_DELETION_FRACTION = 0.05;
/**
* The default behavior of the Unified Genotyper is to allow the genotyping of just one alternate allele in discovery mode; using this flag
* will enable the discovery of multiple alternate alleles. Please note that this works for SNPs only and that it is still highly experimental.
* For advanced users only.
*/
@Advanced
@Argument(fullName = "multiallelic", shortName = "multiallelic", doc = "Allow the discovery of multiple alleles (SNPs only)", required = false)
public boolean MULTI_ALLELIC = false;
// indel-related arguments
/**
* A candidate indel is genotyped (and potentially called) if there are this number of reads with a consensus indel at a site.
@ -132,15 +138,6 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "indelHaplotypeSize", shortName = "indelHSize", doc = "Indel haplotype size", required = false)
public int INDEL_HAPLOTYPE_SIZE = 80;
//gdebug+
// 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 = "bandedIndel", shortName = "bandedIndel", doc = "Banded Indel likelihood computation", required = false)
public boolean BANDED_INDEL_COMPUTATION = false;
@ -153,10 +150,6 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "ignoreSNPAlleles", shortName = "ignoreSNPAlleles", doc = "expt", required = false)
public boolean IGNORE_SNP_ALLELES = false;
@Hidden
@Argument(fullName = "multiallelic", shortName = "multiallelic", doc = "Allow multiple alleles in discovery", required = false)
public boolean MULTI_ALLELIC = false;
/**
* If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
* then this site will be skipped and a warning printed. Note that genotyping sites with many alternate alleles is both CPU and memory intensive.