Add optional minimap2 pass-2 aligner; default behavior unchanged - #2

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cwb14 wants to merge 18 commits into

KGerhardt:masterfrom

cwb14:feat/minimap2

Commits on Apr 24, 2026

swap blast backend for minimap2
cwb14
committed
a2c940f

Commits on Apr 29, 2026

Notes and scripts for 2-pass improvement
cwb14
committed
13760e0

Commits on Apr 30, 2026

Benchmarked minimap2 params
cwb14
committed
e443341
Remove junk
cwb14
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aff2a49

Commits on May 4, 2026

2-pass gap chaining
cwb14
committed
a467ce1
Disable fill_colinear option in process_paf call
cwb14
authored
00da872

Commits on May 6, 2026

Add WFA self-analysis script for PAF summarization
cwb14
authored
e6143d5
IUPAC support
cwb14
committed
df7a0fd

Commits on May 28, 2026

feat: add --pass2-aligner {minimap2,blast}
cwb14
committed
65ed69b

Commits on Jul 9, 2026

Update README with note on default task change
cwb14
authored
94adb61

Commits on Jul 10, 2026

dc-megablast
cwb14
committed
e7fb566

Commits on Jul 28, 2026

Merge upstream KGerhardt/TESorter2 master into fork master
cwb14
committed
1e0a493
Merge upstream TESorter2 master (via fork master) into feat/minimap2
cwb14
committed
a26f1a9
Adopt upstream TEsorter2 branding
cwb14
committed
9675fca

Commits on Aug 7, 2026