Mavis

New Features
- overlay read depth plot density

Improvements
- exon drawing, fixed overlapping exon issues
- additional columns to summary output
- additional metadata for pypi packaging

BugFixes:
- 50 (minor) Was throwing an error that should be ignored when calling by flanking pairs

New features
- ymax and stranded options for overlay diagram read depth plots
- clean up option for aligner output files
- write option for outputting evidence bams, bed files etc (can be turned off now)

Improvements
- Producing products for exact calls where untemplated sequence was not resolved by assuming it is empty
- Caching less transcriptome reads to reduce memory footprint
- break1_split_reads is now entirely distinct from break1_split_reads_forced to show the support better, now if reads with the same name are both target aligned and aligned in the input they will be counted separately (i.e. for mate pairs)

Bugfixes
- (minor) improved resolve by split reads, previously was not resolving unstranded calls because it was assuming the strands represented different resolutions

Improvements

- Additional documentation in the user manual
- Indel calling now includes calling frameshifts
- Additional output files from summary for non-synonymous coding variants
- Made vcf a supported tool to allow loading of general vcf variants when correctly formatted (not requiring a specific tool)

Bug Fixes
- Transcriptome homopolymer filter in the summary stage no longer inappropriately filters translocations

New Features
- Flag for supplementary events
- New filter in summary: homopolymer transcriptome single-bp events
- Added job count information to the checker summary
- Split read call untemplated sequence resolution
- Outputs list of filtered pairs (and reason for filtering) during the clustering stage
- two new transcriptome specific options: trans_min_mapping_quality and trans_fetch_reads_limit

Improvements
- Improved calling compatible events ins vs dup
- Improved error message detection for the checker parsing the log files

Bug Fixes
- Parallel time calculation in the checker previously was summing the max values from libraries where it should have been taking the max of the max
- Now throws an error for missing config file