From 093550a3f24f675964f9197233c90caa24eff5f4 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Jul 2009 20:58:41 +0000
Subject: [PATCH] Removed secondary-base test from SingleSampleGenotyper.  It
 now lives in the variant filtration system.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1302 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/SingleSampleGenotyper.java        | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
index 85a8cbaca..af72f6f0f 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
@@ -24,6 +24,7 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
 import java.util.List;
+import java.util.ArrayList;
 
 @ReadFilters(ZeroMappingQualityReadFilter.class)
 public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate, String> {
@@ -42,7 +43,7 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
     @Argument(fullName = "suppress_metrics", shortName = "printmets", doc = "If specified, don't display metrics", required = false) public Boolean SUPPRESS_METRICS = false;
 
     // Control what features we use in calling variants
-    @Argument(fullName = "ignore_secondary_bases", shortName = "nosb", doc = "Ignore secondary base examination", required = false) public Boolean IGNORE_SECONDARY_BASES = false;
+    //@Argument(fullName = "ignore_secondary_bases", shortName = "nosb", doc = "Ignore secondary base examination", required = false) public Boolean IGNORE_SECONDARY_BASES = false;
     @Argument(fullName = "call_indels", shortName = "indels", doc = "Call indels as well as point mutations", required = false) public Boolean CALL_INDELS = false;
 
     // Control how the genotype hypotheses are weighed
@@ -203,9 +204,11 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
 
         // Handle indels, but don't do anything with the result yet.
         IndelLikelihood I = (CALL_INDELS) ? callIndel(context, reads, offsets) : null;
+        //IndelLikelihood I = (CALL_INDELS) ? callIndel(context, context.getReads(), context.getOffsets()) : null;
 
         // Handle single-base polymorphisms.
         GenotypeLikelihoods G = callGenotype(tracker, ref, pileup, reads, offsets);
+        //GenotypeLikelihoods G = callGenotype(tracker, ref, context);
 
         return G.toAlleleFrequencyEstimate(context.getLocation(), ref, bases.length(), bases, G.likelihoods, sample_name);
     }
@@ -240,9 +243,12 @@ public class SingleSampleGenotyper extends LocusWalker<AlleleFrequencyEstimate,
         }
 
         G.ApplyPrior(ref, this.alt_allele, this.allele_frequency_prior);
-        if (!IGNORE_SECONDARY_BASES && pileup.getBases().length() < 750) {
-            G.applySecondBaseDistributionPrior(pileup.getBases(), pileup.getSecondaryBasePileup());
-        }
+
+        //if (!IGNORE_SECONDARY_BASES && pileup.getBases().length() < 750) {
+        //    G.applySecondBaseDistributionPrior(pileup.getBases(), pileup.getSecondaryBasePileup());
+        //}
+
+        G.applySecondBaseDistributionPrior(pileup.getBases(), pileup.getSecondaryBasePileup());
 
         return G;
     }