From 9c63cee9fcdb69a7a8e8d77a771ddb2afa18f7cd Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 17 Oct 2012 18:36:14 -0400
Subject: [PATCH] Moving pnrm to UnifiedArgumentCollection so it's available
 with the HaplotypeCaller

---
 .../arguments/StandardCallerArgumentCollection.java   | 10 +++++++++-
 .../walkers/genotyper/UnifiedArgumentCollection.java  | 11 +++--------
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
index 9b9f04228..a511364f9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.arguments;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
 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 java.io.File;
@@ -82,7 +83,6 @@ public class StandardCallerArgumentCollection {
     @Argument(shortName = "logExactCalls", doc="x", required=false)
     public File exactCallsLog = null;
 
-
     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!
@@ -97,5 +97,13 @@ public class StandardCallerArgumentCollection {
         this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING;
         this.CONTAMINATION_PERCENTAGE = SCAC.CONTAMINATION_PERCENTAGE;
         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;
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 17137c5e9..abf0b4420 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -27,8 +27,11 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
+<<<<<<< HEAD
 import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
 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.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)
     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
      * 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.IGNORE_LANE_INFO = uac.IGNORE_LANE_INFO;
         this.pairHMM = uac.pairHMM;
-
         // todo- arguments to remove
         this.IGNORE_SNP_ALLELES = uac.IGNORE_SNP_ALLELES;
     }