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Looks like we've got two competing models for an empty interval list: null and 

the empty list.  Score another victory for the integration tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4391 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-09-30 17:11:47 +00:00
parent 78343be52c
commit 1fb8c86f6d
1 changed files with 8 additions and 6 deletions
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14
java/src/org/broadinstitute/sting/gatk/AbstractGenomeAnalysisEngine.java
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@ -161,13 +161,15 @@ public abstract class AbstractGenomeAnalysisEngine {
return;
// if '-L all' was specified, verify that it was the only -L specified and return if so.
for(String interval: argCollection.intervals) {
if(interval.trim().equals("all")) {
if(argCollection.intervals.size() > 1)
throw new UserException("'-L all' was specified along with other intervals or interval lists; the GATK cannot combine '-L all' with other intervals.");
if(argCollection.intervals != null) {
for(String interval: argCollection.intervals) {
if(interval.trim().equals("all")) {
if(argCollection.intervals.size() > 1)
throw new UserException("'-L all' was specified along with other intervals or interval lists; the GATK cannot combine '-L all' with other intervals.");
// '-L all' was specified and seems valid. Return.
return;
// '-L all' was specified and seems valid. Return.
return;
}
}
}