v0.4.6

update broker to use RabbitMQ instead of Redis

v0.4.5

Add AIRR output format and parquet output option

v0.4.4

Bugfix in mongoimport

v0.4.3

update requirements.txt

v0.4.2

Merge pull request #86 from briney/development

Development

v0.4.1

add PyPI automation

v0.4.0

add option to set number of cores (-N, --num-cores)
stop supporting python versions lower than 3.7
general bugfixes

v0.3.3

Features

• updated macaque germline database with germline sequence information from long-read sequencing of the rhesus macaque genome (by Corey Watson and Shane Crotty, publication pending)
• added a second BaseSpace configuration file (~/.basespace/default.cfg) which is designed for use with Illumina's BaseMount. As the BaseSpace Python API is not Python 3 compatible, abstar and abcloud will soon transition to using BaseMount for sequence retrieval rather than the BaseSpace Python API.

Bugfixes

• updated imports in indels.py and mongoimport.py to support Python 3 compatibility

v0.3.1

Python 3.x compatibility

0.2.11

Features

• Added an option (--json-keys) to specify select keys that should be included in the JSON output. Useful if you only want a subset of the default JSON output file. Argument should be a comma-separated list of key names (v_gene,d_gene,j_gene,cdr3_aa)

Bugfixes

• Fixed a bug when attempting to use a custom germline database that was named something other than one of the built-in databases