pipe: Make frameshift repair on by default - #311

Merged

wwood merged 10 commits into

mainfrom

frameshift_repair

Aug 4, 2026

Commits on Aug 1, 2026

pipe: Add --frameshift-repair
wwood
committed
ba67cc5
pipe: Make frameshift repair on by default, add --no-repair-frameshifts

wwood
and
claude
committed
55d509e

Commits on Aug 2, 2026

frameshift_repair: Fix reverse-strand deletion offset, avoid resolving pre-existing Ns

wwood
and
claude
committed
7fb58e7
frameshift_repair: Fix DEFAULT_MAX_DIVERGENCE to match its own tests

wwood
and
claude
committed
4d6ca1d
frameshift_repair: Restore DEFAULT_MAX_DIVERGENCE to 4
wwood
committed
7aecf6e
frameshift_repair: Drop default for run_diamond's repair_frameshifts arg
wwood
committed
bb15b10
frameshift_repair: Drop default for _prefilter's repair_frameshifts arg
wwood
committed
7214063
frameshift_repair: Rename DEFAULT_MAX_DIVERGENCE to DEFAULT_MAX_FRAMESHIFT_REPAIR_DIVERGENCE
wwood
committed
8882fb8
performance_benchmarking: New extra.
wwood
committed
c977549

Commits on Aug 3, 2026

performance_benchmarking: Add to gitignore.
wwood
committed
24552d6