From ba67c7f02bd4ef6fbe6fade9c434c575d30a239b Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 2 Nov 2009 21:09:18 +0000
Subject: [PATCH] added a warning for those using bed files; we properly
 convert bed to the internal representation but the user needs to be aware
 that any output will be one-based closed intervals

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1959 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 99568e3ca..46030847a 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -258,6 +258,8 @@ public class GenomeAnalysisEngine {
             if (new File(interval).exists()) {
                 // support for the bed style interval format
                 if (interval.endsWith(".bed") || interval.endsWith(".BED")) {
+                    Utils.warnUser("Bed files are zero based half open intervals, which are converted to one based closed intervals in the GATK.  " +
+                            "Be aware that all output information and intervals are one based closed intervals.");
                     BedParser parser = new BedParser(new File(interval));
                     locs.addAll(parser.getSortedAndMergedLocations());
                 } else {