Abstar

Bugfixes

Bug Fixes
- Fix logging bug

Bug Fixes

Add `requirements.txt` to `MANIFEST.in`

New Features
- Added documentation for ReadTheDocs
- `abstar.run()` now accepts one or sequences as input not just paths to FASTA/Q files
- updated the human BLASTn database
- Isotype is now a standalone object, added 'unknown' as an isotype option.
- Added `preprocess` module

Bug Fixes
- Improved annotation in cases of extreme V/J trimming
- Improved annotation of region-spanning deletions that result in the deletion of an entire FR or CDR
- Improved parsing of junctions with frameshift indels

New features
- Option for compressed output: `-z, --gzip`
- Option to suppress MongoDB padding from JSON output: `--no-padding`

Bugfixes
- Only concatenates appropriate temp files when building final output (previously, would concat all file in temp directory)
- Only deletes appropriate temp files (previously, would empty the entire temp directory)
- Provide a more useful error message when provided with an invalid FASTQ file (if seq and qual lengths don't match, for example)

Fixed a D-gene assignment bug, resulting from improperly created Sequence objects