Mavis

Improvements
- Ignores invalid reads where there is a cigar string but no aligned portion. Logs a warning

BugFix
- 118: Bugfix files where the delimiter was missing from the header were being reported as empty instead of throwing an error

Improvements
- prints log errors when the validation step was run after annotations (a partial rerun)
- standardization of spanning read calls
- pairing states for transcriptome vs genome using either pairing type (pairing, inferred_pairing)

Bug Fixes
- reference files (with defaults set from environment variables) was still requiring the argument. Now the argument is optional when the default is present
- read evidence undercalled due to strand being set for unstranded sources
- explicit hashing of reads to avoid over-counting

Bugfixes
- Fix for loop during filtering low weight edges in assembly
- Fix for drawing consecutive exons spacing

Improvements
- Style fixes for stricter pycodestyle

Improvements
- Better error messages for config validation errors
- Set 0mq only for non-best blat alignments (even when multiple ties)
- merge data columns when collapsing bpps read from tools
- collect extra breakdancer columns
- greedy algorithm to remove fragment size outliers during call by flanking pairs to avoid coverage too large errors and allow more calls

New Features
- cnvnator support
- breakseq vcf support

Improvements
- masking, dgv_annotation, and template_metadata files are now all optional
- Moved optional dependencies from the install_requires to tests_require and extras_require to improve setup
- Additional documentation and reorganization of the user manual
- Moved the complexity filtering to the summary stage

BugFixes
- Hard clipped read error during read alignment to contig
- vcf input option error where it was not being properly added to the supported tools