Fix gtf bug -- empty string id fields not handled properly
Account for the possibility of negative start coordinates when packing soft-clipped alignments
Make sure that Tribble index is used if one exists
Update na12878kb.jar to one built based on gsa-stable tag 3.0
Update na12878kb.jar to one built based on gsa-stable tag 3.0
Fix "index exists" test.
Add lookup table to allow change to preference keys
Merge remote-tracking branch: upstream/master