From 161c74716c249a08d7adf8985c3036669a71f717 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 15 Jun 2009 14:16:18 +0000
Subject: [PATCH] Forgot to change some direct references to variables in SSG. 
 Fixed.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1009 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/ContrastiveGenotypers.java  | 4 ++--
 .../sting/playground/gatk/walkers/PoolCaller.java             | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java
index bfde40670..04236bf6b 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ContrastiveGenotypers.java
@@ -26,7 +26,7 @@ public class ContrastiveGenotypers extends LocusWalker<Integer, Integer> {
         caller_1b = new SingleSampleGenotyper();
         caller_1b.METRICS_FILE = new File("/dev/stdout");
         caller_1b.METRICS_INTERVAL = 6000;
-        caller_1b.NO_SECONDARY_BASES = false;
+        caller_1b.IGNORE_SECONDARY_BASES = true;
         //caller_1b.retest = false;
         //caller_1b.qHom = 0.04;
         //caller_1b.qHet = 0.49;
@@ -38,7 +38,7 @@ public class ContrastiveGenotypers extends LocusWalker<Integer, Integer> {
         caller_4b = new SingleSampleGenotyper();
         caller_4b.METRICS_FILE = new File("/dev/stdout");
         caller_4b.METRICS_INTERVAL = caller_1b.METRICS_INTERVAL;
-        caller_4b.NO_SECONDARY_BASES = true;
+        caller_4b.IGNORE_SECONDARY_BASES = false;
         //caller_4b.retest = true;
         //caller_4b.qHom = 0.04;
         //caller_4b.qHet = 0.49;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
index 8d3b4e0d6..b19155c5a 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCaller.java
@@ -88,8 +88,8 @@ public class PoolCaller extends LocusWalker<AlleleFrequencyEstimate, String>
 			caller.VARIANTS_FILE = null;
 			caller.METRICS_FILE = null;
             caller.LOD_THRESHOLD = lodThreshold;
-            caller.NO_SECONDARY_BASES = false;
-            caller.PRINT_METRICS = false;
+            caller.IGNORE_SECONDARY_BASES = true;
+            caller.SUPPRESS_METRICS = true;
 			caller.SAMPLE_NAME_REGEX = SAMPLE_NAME_REGEX;
             caller.initialize();
 			caller.variantsOut = individual_output_file;