From 60d54e69f319df02a73d2ead431ffff80c1fd332 Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 12 Apr 2010 01:11:27 +0000 Subject: [PATCH] Hackish fix to present a better error message if the file does not have the proper extension. Will work with Brett to come up with a better solution. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3152 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index c3b41aabf..c00590e85 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -301,6 +301,12 @@ public class GenomeAnalysisEngine { str.toUpperCase().endsWith(".PICARD") || str.toUpperCase().endsWith(".INTERVAL_LIST") || str.toUpperCase().endsWith(".INTERVALS")) return true; + + if(new File(str).exists()) + throw new StingException("Interval argument looks like a filename, but does not have one of " + + "the supported extensions (.bed, .picard, .interval_list, or .intervals). " + + "Please rename your file with the appropriate extension."); + else return false; }