Release 0.6.4

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

Release 0.6.3

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

Release 0.6.2

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

Release 0.6.1

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

Release 0.6.0

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

Release 0.5.0

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

Release 0.4.2

This is version 0.4.2 of covid-spike-classification.

Highlights of this version are:

• OCI container support via Docker Cloud builds (thanks @cmkobel for
  contributing)
• We now report the error probabilities for mutation calls based on the Phred
  score of the mutated bases.

Detailed changes:

Carl Mathias Kobel (1):
      Dockerfile (#6)

Kai Blin (9):
      README: Point docker cloud build status at the right docker hub repo
      core: Track and report error probabilities for all reported mutations
      README: Add note about OCI container route
      README: Link to the source code for the full list of mutations
      chore: Add CI automation, make flake8 happy
      chore: Add CD automation to publish to pypi
      Bump version to 0.4.2
      core: Use more universal space as thousands separator in ratios
      chore: Use right branch for CI tests

Release 0.4.1

This is release 0.4.1 of covid-spike-classification.

This release adds support for using reads in nested input directories or
in zip files containing the reads in directories.

Detailed changes:

Kai Blin (3):
      core: Support finding reads at arbitrary directory depths
      chore: Add more gitignore patterns
      Bump version to 0.4.1

Release 0.4.0

This is release 0.4.0 of covid-spike-classification.

This release adds the telltale mutations for the new VOC/VUIs A.23.1 and
B.1.525 as far as they fall into the sequencing window.

It also reduces the samtools sort memory consumption.

Detailed changes:

Kai Blin (7):
      README: Update tested versions
      README: Clarify that we call mutations, not variants
      core: Make important mutations check more flexible for the future
      core: Add telltale mutations for A.23.1 and B.1.525
      core: limit samtools sort memory consumption
      README: Update install instructions now that we're on bioconda
      Bump version to 0.4.0

Release 0.3.1

This is release 0.3.1 of covid-spike-classification.

This is a bugfix release increasing the robustness of the pileup
parsing for some edge cases.

Detailed changes:

Kai Blin (3):
      README: Add bioconda install link
      core: More robust pileup parsing
      Bump version to 0.3.1