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Don't let users play with the different exact model implementations.

This commit is contained in:
Eric Banks 2013-01-25 10:52:02 -05:00
parent 6dd0e1ddd6
commit f7b80116d6
2 changed files with 8 additions and 8 deletions
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14
protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
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@ -109,13 +109,6 @@ public class StandardCallerArgumentCollection {
@Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
public int MAX_ALTERNATE_ALLELES = 6; public int MAX_ALTERNATE_ALLELES = 6;
/**
* Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
*/
@Advanced
@Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false)
public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel();
/** /**
* If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads. * If this fraction is greater is than zero, the caller will aggressively attempt to remove contamination through biased down-sampling of reads.
* Basically, it will ignore the contamination fraction of reads for each alternate allele. So if the pileup contains N total bases, then we * Basically, it will ignore the contamination fraction of reads for each alternate allele. So if the pileup contains N total bases, then we
@ -125,6 +118,13 @@ public class StandardCallerArgumentCollection {
public double CONTAMINATION_FRACTION = DEFAULT_CONTAMINATION_FRACTION; public double CONTAMINATION_FRACTION = DEFAULT_CONTAMINATION_FRACTION;
public static final double DEFAULT_CONTAMINATION_FRACTION = 0.05; public static final double DEFAULT_CONTAMINATION_FRACTION = 0.05;
/**
* Controls the model used to calculate the probability that a site is variant plus the various sample genotypes in the data at a given locus.
*/
@Hidden
@Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ", required = false)
public AFCalcFactory.Calculation AFmodel = AFCalcFactory.Calculation.getDefaultModel();
@Hidden @Hidden
@Argument(fullName = "logRemovedReadsFromContaminationFiltering", shortName="contaminationLog", required=false) @Argument(fullName = "logRemovedReadsFromContaminationFiltering", shortName="contaminationLog", required=false)
public PrintStream contaminationLog = null; public PrintStream contaminationLog = null;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
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@ -70,7 +70,7 @@ public class AFCalcFactory {
* the needs of the request (i.e., considering ploidy). * the needs of the request (i.e., considering ploidy).
*/ */
public enum Calculation { public enum Calculation {
/** expt. implementation -- for testing only */ /** default implementation */
EXACT_INDEPENDENT(IndependentAllelesDiploidExactAFCalc.class, 2, -1), EXACT_INDEPENDENT(IndependentAllelesDiploidExactAFCalc.class, 2, -1),
/** reference implementation of multi-allelic EXACT model. Extremely slow for many alternate alleles */ /** reference implementation of multi-allelic EXACT model. Extremely slow for many alternate alleles */