Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ganon version 2.1.0 #285

Merged
merged 5 commits into from
Feb 12, 2024
Merged

ganon version 2.1.0 #285

merged 5 commits into from
Feb 12, 2024

Conversation

pirovc
Copy link
Owner

@pirovc pirovc commented Feb 11, 2024

  • --input-target sequence support with --filter-type hibf
  • improved --input-file parsing with more documentation build-ganon unable to read taxonomy file(s) #282
  • parse acc2txid files in chunks, keeping low memory consumption on python side
  • added parameterized tests for --filter-type ibf/hibf on python side

Thanks @jfy133 for reporting!

pirovc and others added 4 commits February 7, 2024 10:34
* split sequences in files for --input-target sequence

* sequence mode, tests, chunk size parsing acc2txid

* fix docs

* docs

* Update tax_util.py

* Update utils.py
* test compile raptor

* attempt with conda

* debug travis

* debug travis

* add tests hibf

* add update
@codecov-commenter
Copy link

codecov-commenter commented Feb 11, 2024

Codecov Report

Attention: 5 lines in your changes are missing coverage. Please review.

Comparison is base (10c1965) 88.56% compared to head (1dfd757) 89.80%.
Report is 1 commits behind head on master.

Files Patch % Lines
src/ganon/build_update.py 94.28% 2 Missing ⚠️
src/ganon/tax_util.py 91.66% 2 Missing ⚠️
src/ganon/util.py 75.00% 1 Missing ⚠️

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #285      +/-   ##
==========================================
+ Coverage   88.56%   89.80%   +1.23%     
==========================================
  Files          23       23              
  Lines        3524     3500      -24     
==========================================
+ Hits         3121     3143      +22     
+ Misses        403      357      -46     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@pirovc pirovc merged commit 68f51b7 into master Feb 12, 2024
1 check passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants