From 96b62daff39a21d478db8d2e443c13e27b863792 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 25 Jan 2012 11:55:33 -0500
Subject: [PATCH] Minor tweak to the warning message.

---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 5f84f62ec..b1495ac7d 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -209,7 +209,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         if ( UAC.OutputMode == UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES &&
                 UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY &&
                 UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.SNP )
-            logger.warn("Note that the EMIT_ALL_SITES option is intended only for point mutations (SNPs) in DISCOVERY mode or generally when running in GENOTYPE_GIVEN_ALLELES mode; it will by no means produce a comprehensive set of indels in DISCOVERY mode");
+            logger.warn("WARNING: note that the EMIT_ALL_SITES option is intended only for point mutations (SNPs) in DISCOVERY mode or generally when running in GENOTYPE_GIVEN_ALLELES mode; it will by no means produce a comprehensive set of indels in DISCOVERY mode");
         
         // get all of the unique sample names
         Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());