From 200f73b008e36bcaabc0cf758fc8c0cf09a07f8c Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 11 Aug 2011 13:44:07 -0400
Subject: [PATCH] No reason to warn the user anymore because it's no longer
 possible for them to specify a dbsnp file on the command-line.

---
 .../recalibration/TableRecalibrationWalker.java     | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index f61fc901b..a044abecb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -29,10 +29,8 @@ import net.sf.samtools.*;
 import net.sf.samtools.util.SequenceUtil;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.Utils;
@@ -155,17 +153,6 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         int lineNumber = 0;
         boolean foundAllCovariates = false;
 
-        // Warn the user if a dbSNP file was specified since it isn't being used here
-        boolean foundDBSNP = false;
-        for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) {
-            if( rod.getName().equalsIgnoreCase(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
-                foundDBSNP = true;
-            }
-        }
-        if( foundDBSNP ) {
-            Utils.warnUser("A dbSNP rod file was specified but TableRecalibrationWalker doesn't make use of it.");
-        }
-
         // Read in the data from the csv file and populate the data map and covariates list
         logger.info( "Reading in the data from input csv file..." );