https://sourceforge.net/p/pb-jelly/blog/2012/08/quick-updates/Recent changes to Quick updatesenThu, 02 Aug 2012 18:13:04 -0000https://sourceforge.net/p/pb-jelly/blog/2012/08/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. Adam EnglishThu, 02 Aug 2012 18:13:04 -0000https://sourceforge.net538b90a5e7d3dabacffaf3c5b7680fa380ab60b6