From f7b80116d6ea5c17d134a17972385709d9237ec2 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 25 Jan 2013 10:52:02 -0500
Subject: [PATCH] Don't let users play with the different exact model
 implementations.

---
 .../StandardCallerArgumentCollection.java          | 14 +++++++-------
 .../walkers/genotyper/afcalc/AFCalcFactory.java    |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
index bb31b410e..3a1532bb1 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
@@ -109,13 +109,6 @@ public class StandardCallerArgumentCollection {
     @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
     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.
      * 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 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
     @Argument(fullName = "logRemovedReadsFromContaminationFiltering", shortName="contaminationLog", required=false)
     public PrintStream contaminationLog = null;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
index 131c1284f..d4bb3cab3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
@@ -70,7 +70,7 @@ public class AFCalcFactory {
      * the needs of the request (i.e., considering ploidy).
      */
     public enum Calculation {
-        /** expt. implementation -- for testing only */
+        /** default implementation */
         EXACT_INDEPENDENT(IndependentAllelesDiploidExactAFCalc.class, 2, -1),
 
         /** reference implementation of multi-allelic EXACT model.  Extremely slow for many alternate alleles */