From e48078b47670c7a0cd5c7a4b25eb4e88929944a7 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 20 May 2009 15:43:26 +0000
Subject: [PATCH] Updated to reflect change to BasecallingReadModel
 constructor.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@760 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/secondarybase/FourBaseRecaller.java  | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java b/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java
index 6f9f2749b..03f7be477 100644
--- a/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java
@@ -38,8 +38,6 @@ public class FourBaseRecaller extends CommandLineProgram {
     public Boolean RAW = false;
     @Argument(fullName="old",         shortName="1", doc="Old Bustard 1.1 mode?", required=false)
     public Boolean OLD = false;
-    @Argument(fullName="context",     shortName="X", doc="Correct for context?", required=false)
-    public Boolean CONTEXT = false;
 
     public static void main(String[] argv) {
         Instance = new FourBaseRecaller();
@@ -70,7 +68,7 @@ public class FourBaseRecaller extends CommandLineProgram {
         fread = ffp.next();
 
         int cycle_offset = (END <= 1) ? 0 : bread.getIntensities().length/2;
-        BasecallingReadModel model = new BasecallingReadModel(bread.getFirstReadSequence().length(), CONTEXT);
+        BasecallingReadModel model = new BasecallingReadModel(bread.getFirstReadSequence().length());
         int queryid;
 
         // learn mean parameters