Covid-spike-classification

This is release 0.6.4 of covid-spike-classification.

This release adds the following mutations:

* L452M as found in various BA.1/BA.2 subtypes
* F486V as found in BA.4/BA.5
* Q677E as found in BA.2.3.1
* S704L as found in BA.1.9

Detailed changes:

Kai Blin (5):
core: Add F486V mutation call
core: Add L452M mutation call
core: Add S704L mutation call
core: Add Q677E mutation call
Bump version to 0.6.4

This is release 0.6.3 of covid-spike-classification

This release adds the Q493R mutation found in the Omicron BA.1 subtype.

Detailed changes:


Kai Blin (2):
core: Add Q493R mutation call
Bump version to 0.6.3

This is release 0.6.2 of covid-spike-classification.

The main changes are the added support for the mutations seen in B.1.1.529 and
B.1.640.

Detailed changes:


Kai Blin (12):
core: Add N440K mutation call
core: Add G446S mutation call
core: Add Y449N mutation call
core: Add E484A mutation call
core: Add F490R mutation call
core: Add Q493K mutation call
core: Add G496S mutation call
core: Add Q498R mutation call
core: Add Y505H mutation call
core: Add T547K mutation call
core: Add N679K mutation call
Bump version to 0.6.2

This is release 0.6.1 of covid-spike-classification.

The main change is the added support for the Y449H mutation seen in C.1.2.

Detailed changes:

Kai Blin (4):
core: Add Y449H mutation call
chore: Make shellcheck happy for the generator script
chore: Make new flake8 happy
Bump version to 0.6.1

This is release 0.6.0 of covid-spike-classification

The main features of this version are:
* Added support for K417T and T732A mutation calls
* Mutations are now fully ordered in the output, we don't treat a handful of
mutations as special by listing them first anymore

Detailed changes:

Kai Blin (10):
README: Add reference to the paper
core: Just sort regions by position
core: Add K417T mutation
chore: Run lint/tests from a makefile for easier local testing
chore: Add missing K417T test file
core: Add T732A mutation call
chore: Make flake8 happy on the test files
tests: Make sure we don't miss test files in future
chore: Add more things to the gitignore file
Bump version to 0.6.0

This is release 0.5.0 of covid-spike-classification

This release adds detection logic for more mutations:
- K417N
- T478K
- T478R
- E484Q

Additionally, new tests make sure all of these mutations are detected
properly.

Detailed changes:

Kai Blin (14):
README: Fix a typo
core: Add additional mutation checks
core: Add option to silence D614G warning
core: Also list D614G in the comment
chore: Add integration test support
chore: Try to get conda to work in GitHub actions
chore: More conda activation fun
chore: Use setup-miniconda action to get conda set up
chore: More integration test fixes
chore: Try to diagnose integration test failure on GitHub
chore: mode integration test debugging
chore: One more attempt to get integration tests to work
chore: Remove integration test debugging logic
Bump version to 0.5.0