From 66a4de9a1d3d931293ab351eaeeb09e2e031c610 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 18 Sep 2009 03:23:30 +0000 Subject: [PATCH] Genotype check should be case-insensitive git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1649 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/playground/gatk/walkers/concordance/SimpleVenn.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java index b02602bbf..f454e1e52 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SimpleVenn.java @@ -55,7 +55,7 @@ public class SimpleVenn implements ConcordanceType { printVariant(set2_writer, call2); // intersection (concordant) - else if ( call1.getAltBasesFWD().equals(call2.getAltBasesFWD()) ) + else if ( call1.getAltBasesFWD().equalsIgnoreCase(call2.getAltBasesFWD()) ) printVariant(intersect_writer, call1); // intersection (discordant) @@ -74,4 +74,4 @@ public class SimpleVenn implements ConcordanceType { set1_writer.close(); set2_writer.close(); } -} \ No newline at end of file +}