Version 0.4.4

What's Changed

• can now parse new HIVDB files
• added support for intel MacOS

Full Changelog: v0.4.3...v0.4.4

Version 0.4.3

New Features

• added new args to specify files necessary for isSDRM, isApobecMutation, isUnusual, and primaryType #117
• added new args to specify where to write output files from the updater -updater_outdir

Bug Fixes

• fixed issue where isSDRM was missing from mutdict
• fixed issue where X amino acid was triggering isSDRM incorrectly
• included directions, and subsequently fixed, --forceupdate

Version 0.4.2

• Added binaries for Post-align and Minimap2 (#115)
• Fixed issues with displaying AAs in the drug resistance fields (#112)
• Fixed issue with referencing IN mutations documention on HivDB webstite (#105)

Version 0.4

• deprecated subtyper.py script, subtyping is no longer supported
• handle ambiguous codons (#72)
• added reference/ genotype update scripts (b4a1fc0)
• bug fixes (#92, #99)

Version 0.3

What's Changed

• Use submodule to retrieve data files by @GopiGugan in #68
• Update dev branch with recent changes by @GopiGugan in #78
• Adding Postalign as Alignment Program by @WilliamZekaiWang in #83
• Switch to postalign and updating unit tests, resources by @ArtPoon in #82
• Adding subtyping option and fixes to -json by @WilliamZekaiWang in #86
• Updating Post-align Dependencies by @WilliamZekaiWang in #88

New Contributors

• @GopiGugan made their first contribution in #68
• @WilliamZekaiWang made their first contribution in #83

Full Changelog: v0.2.1...v0.3

Version 0.2.1

Bug fix

Version 0.2.0

The updater.py script is now deprecated due to changes in the HIVdb website.

Re-release of v0.1.2 for JOSS

• Added CONTRIBUTING.md file
• Added /paper containing manuscript files for submission to JOSS

v0.1.2

• package includes NucAmino binaries
• fixed subtyping
• parsing JSON output from NucAmino to address full-length pol issue
• writes temporary alignment file to screen for illegal characters
• separating alignment data by gene
• wrote detailed installation instructions

v.0.0.2

• ported HIV subtyping from HIVdb pipeline
• setup script sets user permissions for system installation to allow users to access downloaded resources
• moved gui.py to a separate branch as a work in progress
• extensive refactoring and application of PEP8 code style
• byte string conversion to accommodate Python 3.5
• moved FASTA parsing to utils.py
• fixes #44, #42