Replace the map-of-lists mate-finding data structure with a much more efficient hashmap. This prevents long stalls when a large number of as-yet-unpaired mates are looking for the same genome offset.
Don't blank the skipped.gtf file when running in reference guided mode.
Don't try to look up reference scaffolds in a depth-of-coverage map; this leads to undefined behaviour.
Merge pull request #1 from smowton/master

Pre-github smowton patches
Merge branch 'master' of https://github.com/cole-trapnell-lab/cufflinks into develop

get changes from upstream