Mavis

Bug Fixes
- empty tab file error fix

Improvements
- set checker exit status
- improved error message on bad input directory for checker
- removed samtools as dependency (using only pysam now)

New Features
- convert option for the config command now accepts a variable number of input files to be converted
- sequence complexity filtering option
- Added mail options for slurm/sge

Improvements
- Added a more complex pipeline example to the documentation
- Added short contig assembly test
- Breakpoint distance pairing now accounts for untemplated sequence
- blat_rank has been renamed to alignment_rank and is now calculated for both bwa and blat
- alignment_rank is used to filter contig alignments so that there is only one contig alignment per contig
- Removed any unnecessary parameters
- checker is now detecting command not found errors
- filters spanning read alignments using the min contig score parameter (same filtering done on contigs)

BugFixes
- Filtering contig alignments was getting highest rank instead of lowest. Best ranks are lower ranks
- logs version for the configured aligner instead of just blat

BugFix
- fixes error associated with drawing small exons at the start or end of a fusion transcript not being included in the interval mapping

BugFixes:
- fixed interval error for single bp exon/insertion drawings

New Features
- small insertions/novel exons are now drawn taller than the surrounding exons
- small exons are not labelled and therefore not required to be the min object size
- added the new configurable drawing parameter `exon_min_focus_size` to determine a 'small' exon
- 'small' exons in the fusion transcript add the sequence to their labels

BugFixes
- fixed annotations loading bug in auto-generating configs for transcriptomes libraries

Minor BugFix
- config loading was not backwards compatible with older configs. Fixed so 1.6.6 can read configs from previous mavis versions as well