From 2eb5d9b2d230c65f3e04fe1f8e9d3d733960d3c2 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 16 Sep 2010 18:53:42 +0000
Subject: [PATCH] CountCovariates makes sure that it sees a rod type that it
 expects for use as a variant mask (accepted types are dbsnp, vcf, and bed)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4296 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../recalibration/CovariateCounterWalker.java      | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
index d5a3b118b..0df273eab 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -25,7 +25,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
+import org.broad.tribble.bed.BEDCodec;
+import org.broad.tribble.dbsnp.DbSNPCodec;
 import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broad.tribble.vcf.VCFCodec;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -179,12 +182,16 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
             System.exit( 0 ); // Early exit here because user requested it
         }
 
-        // Warn the user if no dbSNP file was specified
+        // Warn the user if no dbSNP file or other variant mask was specified
         boolean foundDBSNP = false;
         for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) {
             if( rod != null ) {
-                foundDBSNP = true;
-                break;
+                if( rod.getReferenceOrderedData().getType().equals(DbSNPCodec.class) ||
+                        rod.getReferenceOrderedData().getType().equals(VCFCodec.class) ||
+                        rod.getReferenceOrderedData().getType().equals(BEDCodec.class) ) {
+                    foundDBSNP = true;
+                    break;
+                }
             }
         }
         if( !foundDBSNP && !RUN_WITHOUT_DBSNP ) {
@@ -381,6 +388,7 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
      *   adding one to the number of observations and potentially one to the number of mismatches
      * Lots of things are passed as parameters to this method as a strategy for optimizing the covariate.getValue calls
      *   because pulling things out of the SAMRecord is an expensive operation.
+     * @param counter Data structure which holds the counted bases
      * @param gatkRead The SAMRecord holding all the data for this read
      * @param offset The offset in the read for this locus
      * @param refBase The reference base at this locus