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Moving pnrm to UnifiedArgumentCollection so it's available with the HaplotypeCaller

This commit is contained in:
Mark DePristo 2012-10-17 18:36:14 -04:00
parent e9b7324dc1
commit 9c63cee9fc
2 changed files with 12 additions and 9 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
View File

@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.arguments;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.io.File; import java.io.File;
@ -82,7 +83,6 @@ public class StandardCallerArgumentCollection {
@Argument(shortName = "logExactCalls", doc="x", required=false) @Argument(shortName = "logExactCalls", doc="x", required=false)
public File exactCallsLog = null; public File exactCallsLog = null;
public StandardCallerArgumentCollection() { } public StandardCallerArgumentCollection() { }
// Developers must remember to add any newly added arguments to the list here as well otherwise they won't get changed from their default value! // Developers must remember to add any newly added arguments to the list here as well otherwise they won't get changed from their default value!
@ -97,5 +97,13 @@ public class StandardCallerArgumentCollection {
this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING; this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING;
this.CONTAMINATION_PERCENTAGE = SCAC.CONTAMINATION_PERCENTAGE; this.CONTAMINATION_PERCENTAGE = SCAC.CONTAMINATION_PERCENTAGE;
this.exactCallsLog = SCAC.exactCallsLog; this.exactCallsLog = SCAC.exactCallsLog;
this.AFmodel = SCAC.AFmodel;
} }
/**
* 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.EXACT;
} }

11
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -27,8 +27,11 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection; import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
<<<<<<< HEAD
import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory; import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
import org.broadinstitute.sting.utils.pairhmm.PairHMM; import org.broadinstitute.sting.utils.pairhmm.PairHMM;
=======
>>>>>>> 19181ee... Moving pnrm to UnifiedArgumentCollection so it's available with the HaplotypeCaller
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@ -38,13 +41,6 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
@Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- SNP is the default option, while INDEL is also available for calling indels and BOTH is available for calling both together", required = false) @Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- SNP is the default option, while INDEL is also available for calling indels and BOTH is available for calling both together", required = false)
public GenotypeLikelihoodsCalculationModel.Model GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP; public GenotypeLikelihoodsCalculationModel.Model GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP;
/**
* 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.EXACT;
/** /**
* The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily * The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily
* distinguish between PCR errors vs. sequencing errors. The practical implication for this value is that it * distinguish between PCR errors vs. sequencing errors. The practical implication for this value is that it
@ -219,7 +215,6 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
this.EXCLUDE_FILTERED_REFERENCE_SITES = uac.EXCLUDE_FILTERED_REFERENCE_SITES; this.EXCLUDE_FILTERED_REFERENCE_SITES = uac.EXCLUDE_FILTERED_REFERENCE_SITES;
this.IGNORE_LANE_INFO = uac.IGNORE_LANE_INFO; this.IGNORE_LANE_INFO = uac.IGNORE_LANE_INFO;
this.pairHMM = uac.pairHMM; this.pairHMM = uac.pairHMM;
// todo- arguments to remove // todo- arguments to remove
this.IGNORE_SNP_ALLELES = uac.IGNORE_SNP_ALLELES; this.IGNORE_SNP_ALLELES = uac.IGNORE_SNP_ALLELES;
} }