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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
This commit is contained in:
aaron 2009-11-02 21:09:18 +00:00
parent b71b66bd88
commit ba67c7f02b
1 changed files with 2 additions and 0 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -258,6 +258,8 @@ public class GenomeAnalysisEngine {
if (new File(interval).exists()) { if (new File(interval).exists()) {
// support for the bed style interval format // support for the bed style interval format
if (interval.endsWith(".bed") || interval.endsWith(".BED")) { 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)); BedParser parser = new BedParser(new File(interval));
locs.addAll(parser.getSortedAndMergedLocations()); locs.addAll(parser.getSortedAndMergedLocations());
} else { } else {