Adding the sylph coverage model to yacht by rtraborn · Pull Request #141 · KoslickiLab/YACHT

Commits on Jan 12, 2026

Added winner map functionality to hypothesis_recovery_src.py.

R. Taylor Raborn
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R. Taylor Raborn
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Minor update to .gitignore.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Jan 14, 2026

Updated utils.py to define MIN_ANI_THRESHOLD.

R. Taylor Raborn
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R. Taylor Raborn
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Added parallelization to the coverage calculation; should increase speed.

R. Taylor Raborn
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Cleaning up documentation.

R. Taylor Raborn
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Added sample_sig as a pool variable to remove big performance overheads.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Jan 15, 2026

Improvements to parallel processing and new arguments for the winner-takes-all k-mer reassignment.

R. Taylor Raborn
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R. Taylor Raborn
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Small tweaks to help statement for new winner-map related arguments.

R. Taylor Raborn
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R. Taylor Raborn
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Fixed a small typo.

R. Taylor Raborn
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Renamed MEDIAN_ANI_THRESHOLD to avoid confusion.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Jan 16, 2026

Fixed critical bug due to umap_unordered- now matching on organism name.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Jan 27, 2026

Added ANI-capping utility to avoid biologically impossible ANI inflation due to low lambda.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Jan 28, 2026

Updated cov_calc to cap ANIs at 1.0; pt II of ani capping.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Jan 29, 2026

Removed old commented code that was replaced by the winner-map addition.

R. Taylor Raborn
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R. Taylor Raborn
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Updated ANI adjustment to avoid ANI adjustment under high-coverage, update to median_ani_threshold.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Mar 12, 2026

Patched a minor bug relating to performance of python's gzip on Mac OS, replacing it with the system gzip

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Mar 13, 2026

Added two-pass mode to --winner-take-all procedure.

R. Taylor Raborn
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R. Taylor Raborn
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Various updates to run_YACHT, including adding yacht-level arugments --calculate-coverage and --no_two_pass.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Apr 7, 2026

Removed excessive comments in the threshold filtering step.

R. Taylor Raborn
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R. Taylor Raborn
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Bookmarked code to fix for tomorrow.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Apr 9, 2026

Updates for code review.

R. Taylor Raborn
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R. Taylor Raborn
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Draft re-normalization procedure.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Apr 10, 2026

Completed re-normalization procedure for rel_abund column in output.

R. Taylor Raborn
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Added re-norm for times when wta is on but calc. cov. is off.

R. Taylor Raborn
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R. Taylor Raborn
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Fixed tab issue.

R. Taylor Raborn
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Removed print statements.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Apr 14, 2026

Small change to how organism_id_list is created to accomodate gtdb genomes during yacht convert.

R. Taylor Raborn
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R. Taylor Raborn
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Commits on Apr 15, 2026

Improvements to yacht convert functionality with cov_calc output.

R. Taylor Raborn
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R. Taylor Raborn
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Replaced counts with weights for yacht convert when paired with calculate_coverage sheets. Added various handling improvements, including a clear help message.

R. Taylor Raborn
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R. Taylor Raborn
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Uh oh!

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