From 659b82e74d04c0cc6f083b14b313155812a4b95e Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 2 Apr 2012 22:25:16 -0400
Subject: [PATCH] Old -B syntax is long gone at this point.  Safe to remove the
 warning.

---
 .../sting/gatk/CommandLineExecutable.java         | 15 ---------------
 .../gatk/arguments/GATKArgumentCollection.java    |  5 -----
 2 files changed, 20 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
index e5aaf2338..c6bb4a27c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
@@ -103,21 +103,6 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
             argumentSources.add(walker);
 
             Collection<RMDTriplet> rodBindings = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
-
-            // todo: remove me when the old style system is removed
-            if ( getArgumentCollection().RODBindings.size() > 0 ) {
-                logger.warn("################################################################################");
-                logger.warn("################################################################################");
-                logger.warn("Deprecated -B rod binding syntax detected.  This syntax has been eliminated in GATK 1.2.");
-                logger.warn("Please use arguments defined by each specific walker instead.");
-                for ( String oldStyleRodBinding : getArgumentCollection().RODBindings ) {
-                    logger.warn("  -B rod binding with value " + oldStyleRodBinding + " tags: " + parser.getTags(oldStyleRodBinding).getPositionalTags());
-                }
-                logger.warn("################################################################################");
-                logger.warn("################################################################################");
-                System.exit(1);
-            }
-
             engine.setReferenceMetaDataFiles(rodBindings);
 
             for (ReadFilter filter: filters) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 02d211a0c..670f04bda 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -107,11 +107,6 @@ public class GATKArgumentCollection {
     @Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
     public File referenceFile = null;
 
-    @Deprecated
-    @Hidden
-    @Input(fullName = "rodBind", shortName = "B", doc = "Bindings for reference-ordered data, in the form :<name>,<type> <file>", required = false)
-    public ArrayList<String> RODBindings = new ArrayList<String>();
-
     @Argument(fullName = "nonDeterministicRandomSeed", shortName = "ndrs", doc = "Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run", required = false)
     public boolean nonDeterministicRandomSeed = false;