CLI + output parity: SAM/SJ/read-input knobs and the STAR limit surface

[BenjaminDEMAILLE]

CLI and output parity: 31 STAR 2.7.11b parameters, and a test that makes the parameter surface a machine-checked number.

What changed

tests/parameter_surface.rs checks every parameter name STAR 2.7.11b accepts against what clap recognises. The name list is every column-1 name of STAR's parametersDefault, with none removed: 203 names, interface only, no STAR source.

Two supporting lists stop "accepted" from meaning "implemented":

• ACCEPTED_BUT_INERT — 22 knobs that parse but change no output byte, each with its reason. A second test asserts the CLI does accept them, so the annotation cannot drift.
• NOT_YET_ACCEPTED — the 26 still missing, grouped by the theme that will bring them.

The test fails in both directions: an unrecognised name that is not declared missing fails, and a name still listed as missing that has since been implemented also fails.

145/203 to 175/203 accepted, both measured by running the test.

Flags that do something:

Flag	Behaviour
--outSAMmode None	routes to the null writer; SJ.out.tab, Log.final.out and counts are still produced, only records are dropped
--outSAMmode NoQS	strips quality strings
--outSJtype None	suppresses SJ.out.tab
--outSJfilterReads Unique	only unique reads count towards outSJfilter*, so a junction supported solely by multimappers drops out
--outSAMheaderHD / PG / CommentFile	build @hd, extra @pg and @co, with TAG:value validated rather than passed through
--readFilesPrefix	applied during parsing, so every consumer sees final paths
--readQualityScoreBase, --outQSconversionAdd	one signed shift applied as the FASTQ is read, normalising to Phred+33 once
--readNameSeparator	cuts read names at the first separator

Why

Correction to the previous revision of this description

The earlier fixture removed parametersFiles, sysShell and versionGenome from the name list, calling them non-user meta-parameters. All three are settable on STAR's command line like any other, so dropping them did not describe a narrower surface: it hid three names this branch does not accept and shrank the denominator the coverage figure is quoted against. The fixture is now STAR's complete list, the three sit in NOT_YET_ACCEPTED, and the numbers above moved accordingly.

clap rejecting them is deliberate and stays that way for now. Silently accepting --parametersFiles would discard every parameter in the file the user passed, which is worse than an error.

Parameter coverage was a claim in prose. A test makes it a number that cannot drift, and the grouped NOT_YET_ACCEPTED list makes the remaining gap legible rather than a bare count.

NoQS is a decorator around the boxed writer rather than a branch at each of the five record-building sites, so the clone is paid only when the flag is set.

One output change at default settings

STAR's default --readNameSeparator is / and STAR cuts there; this codebase did not. Verified on this branch as submitted, aligning 1000 yeast reads whose names carry a /1 suffix, against STAR 2.7.11b:

STAR          ERR12389696.12376817
origin/main   ERR12389696.12376817/1
this branch   ERR12389696.12376817      <- matches STAR

Everything else is unchanged: on the 10k yeast SE tier, where no read name contains a /, this branch and origin/main produce byte-identical SAM records (9724 each, differing only in the @PG CL: line, which records the binary path).

Verification

Gate green: lib + integration tests, clippy -D warnings, cargo fmt --check, MSRV 1.89. New integration tests cover each implemented flag; the surface test covers the rest.

Bookkeeping note: four flags in NOT_YET_ACCEPTED here (--genomeType, --genomeTransformOutput, --genomeSuffixLengthMax, --sjdbInsertSave) are implemented on #109. Whichever merges second moves them out of the list in the same commit.