Fix for opening local BAM files for non registered files
@@ -389,11 +389,11 @@ public final class Utils {
}
notRegisteredFile.setPath(processUrl(fileUrl));
notRegisteredFile.setCompressed(false);
- notRegisteredFile.setType(BiologicalDataItemResourceType.URL);
+ notRegisteredFile.setType(BiologicalDataItemResourceType.getTypeFromPath(fileUrl));
notRegisteredFile.setReferenceId(chromosome.getReferenceId());
BiologicalDataItem index = new BiologicalDataItem();
- index.setType(BiologicalDataItemResourceType.URL);
+ index.setType(BiologicalDataItemResourceType.getTypeFromPath(indexUrl));
index.setPath(processUrl(indexUrl));
notRegisteredFile.setIndex(index);
return notRegisteredFile;
