Conversation
Integrate minibwa (https://github.com/lh3/minibwa) as a `-p minibwa` mapping option, modelled on the existing BWA integration since minibwa is BWT-based and requires a pre-built index. - Index: `minibwa index [-t N] <ref.fa> <out.prefix>` (prefix is a positional argument, not `-p`), producing `.l2b` and `.mbw` files. - Map: `minibwa map -t N <idx> <r1> [r2]`. - Version check uses the `minibwa version` subcommand (e.g. `0.2-r370`); `minibwa --version` is not recognised. - Reject `--interleaved` input: minibwa has no interleaved-pairing option. Add minibwa to the pixi environment for linux-64 and osx-64 (it is not available on osx-arm64). Remove dashing, which hard-pins zlib<1.3 and so conflicts with minibwa's libzlib>=1.3.2; dashing was only an optional galah precluster method (skani is the default). Add assert_cli tests for coupled-read mapping and interleaved rejection. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Integrate minibwa (https://github.com/lh3/minibwa) as a
-p minibwamapping option, modelled on the existing BWA integration since minibwa is BWT-based and requires a pre-built index.minibwa index [-t N] <ref.fa> <out.prefix>(prefix is a positional argument, not-p), producing.l2band.mbwfiles.minibwa map -t N <idx> <r1> [r2].minibwa versionsubcommand (e.g.0.2-r370);minibwa --versionis not recognised.--interleavedinput: minibwa has no interleaved-pairing option.Add minibwa to the pixi environment for linux-64 and osx-64 (it is not available on osx-arm64). Remove dashing, which hard-pins zlib<1.3 and so conflicts with minibwa's libzlib>=1.3.2; dashing was only an optional galah precluster method (skani is the default).
Add assert_cli tests for coupled-read mapping and interleaved rejection.