Skip to content

Conversation

@not-a-feature
Copy link

This PR adresses #84 by introducing support for InDels.
The implementation aims to replicate the behavior of bcftools consensus.

Currently, the feature is enabled by default. To ensure backward compatibility, we could introduce a flag (defaulting to false) that allows users to omit InDels if needed.

I didn't have the time to perform some performance evaluation.
Feel free to keep open for further testing and validation.

@codecov
Copy link

codecov bot commented Sep 12, 2025

Codecov Report

❌ Patch coverage is 73.91304% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.69%. Comparing base (0f97b76) to head (9705175).

Files with missing lines Patch % Lines
pyfaidx/__init__.py 73.91% 6 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #240      +/-   ##
==========================================
- Coverage   88.81%   88.69%   -0.13%     
==========================================
  Files           2        2              
  Lines        1118     1132      +14     
==========================================
+ Hits          993     1004      +11     
- Misses        125      128       +3     

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

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@mdshw5
Copy link
Owner

mdshw5 commented Sep 13, 2025

Thanks for taking the time to implement this @not-a-feature. It's not a simple feature, and I want to take a bit of time to understand what you've done here before merging, but at first glance I really appreciate what you've done here. I also notice that bcftools consensus has a giant test suite that likely has some good tests if the goal is to implement similar behavior.

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