Add optional minimap2 pass-2 aligner; default behavior unchanged - #2
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cwb14 wants to merge 18 commits into
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Add optional minimap2 pass-2 aligner; default behavior unchanged#2cwb14 wants to merge 18 commits into
cwb14 wants to merge 18 commits into
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This script summarizes self-alignment PAF data, producing best per query, reciprocal best hits, and clusters files. It includes functionality for parsing CIGAR strings and calculating metrics based on alignment data.
Added note about switching default task to dc-megablast.
# Conflicts: # README.md
# Conflicts: # README.md # tesorter2/blast_pass2.py # tesorter2/pipeline.py
Upstream renamed the project TEsorter2; the fork now follows. README and in-package docstrings/help text updated. The dated run memo under docs/runs/ keeps its original names and paths so the recorded commands stay reproducible, with a note pointing at the rename.
# Conflicts: # tesorter2/pipeline.py
…blast-task Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
minimap2 and the 70-70-70 rule remain available as opt-ins (--pass2-aligner minimap2, -rule 70-70-70). tesorter_compat gains --pass2-aligner so the minimap2 path stays reachable there. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
WFA_TEsorter (+ source and scripts), eval.py, classify_final.py, and docs/runs/memo.md were the toolchain for tuning the minimap2 pass-2; nothing imports or invokes them. Git history preserves them. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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This allows users to input a library of known LTR-RTs to aid in annotation during pass-2. It also adds flexibility for using minimap2 for pass-2, which seems faster and similarly accurate in some circumstances. The default run is unchanged: blastn pass-2 with the 80-80-80 rule, exactly as on master. I verified default function is unchanged.