cli parity #147 with fixes - #216

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Psy-Fer merged 8 commits into

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batch/cli-parity

Aug 7, 2026

Commits on Aug 7, 2026

test(cli): lock the STAR 2.7.11b parameter surface, and declare the 31 knobs this PR covers

authored and
Psy-Fer
committed
aeaa716
feat(cli): SAM/SJ/read-input knobs, and cut read names at the separator as STAR does

authored and
Psy-Fer
committed
f855695
test(cli): end-to-end coverage for the new knobs, plus changelog

authored and
Psy-Fer
committed
e70b305
chore: rebase onto #145, dropping the outSAMorder declaration it now owns

authored and
Psy-Fer
committed
b6ca7e4
test(params): stop excluding three STAR parameters from the surface fixture

BenjaminDEMAILLE
authored and
Psy-Fer
committed
de9f591
test(params): unlist two implemented parameters, clear three stale ones
Psy-Fer
committed
9707a7f
fix(sj): --outSJfilterReads Unique must exclude multimappers at record
Psy-Fer
committed
bea2faf
test(cli): assert the QNAME --readNameSeparator actually emits
Psy-Fer
committed
fdf13a6