Version 2.2.0

1. Fixed bugs in novel end detection; novel ends must not be on CGP. Split up the flags to a boolean and a distance.
2. Fixed an issue when IsoSeq was given to some genomes but not at all.
3. Reverted hal2fasta changes to match changes to the hal toolkit.
4. Removed the automated singularity testing because it stopped working.
5. Tried to add a new dockerfile for a more complete image, but it was not passing in travis. it now lives in the repo as an experimental dockerfile.