From 1994c3e3bca05593d05693dd41de7bf30b21cbec Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 16 Dec 2011 16:33:13 -0500
Subject: [PATCH] Only print warning about allele incompatibility when running
 there are genotypes in the file in CombineVariants

---
 .../sting/utils/variantcontext/VariantContextUtils.java      | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index 91a018c4e..c9a4965c1 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -619,8 +619,9 @@ public class VariantContextUtils {
             if (vc.alleles.size() == 1)
                 continue;
             if ( hasPLIncompatibleAlleles(alleles, vc.alleles)) {
-                logger.warn(String.format("Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s",
-                        genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles));
+                if ( ! genotypes.isEmpty() )
+                    logger.warn(String.format("Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s",
+                            genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles));
                 genotypes = stripPLs(genotypes);
                 // this will remove stale AC,AF attributed from vc
                 calculateChromosomeCounts(vc, attributes, true);