Quick updates

Unfortunately, testing for PBJelly 12.7.25 wasn't as rigorous as it needed to be and there were a number of bugs that slipped through. These have been addressed and are now in the CHANGELOG file distributed with PBJelly 12.8.2. Sorry for any inconvenience this may have caused.

Upgrades
-- Gaps that are within 25 bp of one another are now consolidated into a single gap.
-- Made some progress on the scripts that help with NCBI Submission of Upgraded Genomes (Still in Beta, though)

Bug Fixes
-- summarizeAssembly.py didn't handle references without contigs/gaps in an elegant way - It is now prepared to deal with such cases.
-- Collection.py was recently upgraded to make use of the LiftOverTable objects. An untested side-affect was that Collection.py created .qual file outputs that were in a bad format.
-- An R&D AssemblyAssessor method to compare metrics made it into the distributed code. This caused a few gap to not report the best filling metrics
-- sawriter was being called to index the .contigs.fasta instead of the scaffolding.fasta which caused the mapping stage to fail.
-- Fixed the handling of strandedness in M4 and M5 Alignments.