return new FilePointer(IntervalMergingRule.ALL);
}
Map<SAMReaderID, List<GATKChunk>> fileChunks = new HashMap<SAMReaderID, List<GATKChunk>>();
List<GenomeLoc> locations = new ArrayList<GenomeLoc>();
IntervalMergingRule mergeRule = filePointers.get(0).getIntervalMergingRule();
// First extract all intervals and file chunks from the FilePointers into unsorted, unmerged collections
for ( FilePointer filePointer : filePointers ) {
locations.addAll(filePointer.getLocations());
if (mergeRule != filePointer.getIntervalMergingRule())