From bb7a37e8f2c8911f95ccacf305175cf30bca0302 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 29 Aug 2011 13:19:35 -0400
Subject: [PATCH] We need to allow reference calls in the input VCF for the
 GenotypeAndValidate walker when using the BAM as truth so that we can test
 supposed monomorphic calls against the truth.

---
 .../walkers/validation/GenotypeAndValidateWalker.java  | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
index 2b38afaf6..00a506fab 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
@@ -347,12 +347,14 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
         }
 
         VariantCallContext call;
-        if ( vcComp.isSNP() )
+        if ( vcComp.isSNP() ) {
             call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
-        else if ( vcComp.isIndel() ) {
+        } else if ( vcComp.isIndel() ) {
             call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
-        }
-        else {
+        } else if ( bamIsTruth ) {
+            // assume it's a SNP if no variation is present; this is necessary so that we can test supposed monomorphic sites against the truth bam
+            call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
+        } else {
             logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
             return counter;
         }