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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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2
java/src/org/broadinstitute/sting/gatk/AbstractGenomeAnalysisEngine.java
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@ -161,6 +161,7 @@ public abstract class AbstractGenomeAnalysisEngine {
return; return;
// if '-L all' was specified, verify that it was the only -L specified and return if so. // if '-L all' was specified, verify that it was the only -L specified and return if so.
if(argCollection.intervals != null) {
for(String interval: argCollection.intervals) { for(String interval: argCollection.intervals) {
if(interval.trim().equals("all")) { if(interval.trim().equals("all")) {
if(argCollection.intervals.size() > 1) if(argCollection.intervals.size() > 1)
@ -170,6 +171,7 @@ public abstract class AbstractGenomeAnalysisEngine {
return; return;
} }
} }
}
// if include argument isn't given, create new set of all possible intervals // if include argument isn't given, create new set of all possible intervals
GenomeLocSortedSet includeSortedSet = (argCollection.intervals == null && argCollection.RODToInterval == null ? GenomeLocSortedSet includeSortedSet = (argCollection.intervals == null && argCollection.RODToInterval == null ?