[RobbinBouwmeester]

Reads a Thermo .raw directly instead of converting it to mzML first. This is opt-in at two levels: a Cargo feature (thermo) that no release build enables, and a configuration key (convert.thermo_native, default false).

How it works

• mzdata's thermo feature hosts Thermo's RawFileReader on a .NET 8 runtime.
• raw::ensure_mzml passes the .raw through under convert.thermo_native. convert reads it with vendor centroiding, the same peak picking ThermoRawFileParser applies by default.
• One thread reads the file, which RawFileReader does serially. The thread pool decodes the spectra in batches, folded back in file order; the output is byte-identical to a one-thread decode.
• Spectra that arrive as a centroid list without signal arrays are handled in peaks_of. The mzML path is unchanged.
• The instrument comes from the file's metadata. instrument::from_configurations skips the serial number and the instrument-method text that mzdata stores as customization, so the Astral defaults apply as they do for an mzML.
• Reports record params.reader = "thermorawfilereader" and params.centroiding = "vendor".
• A build without the feature refuses convert.thermo_native with a message rather than falling back to a converter.

Measured against ThermoRawFileParser 1.4.5 on PXD071205 Astral files (docs/04_convert.md, "Native Thermo reading"):

	native	via ThermoRawFileParser
one 15 min file	2,022 MS1 / 188,011 MS2 spectra, 250 windows	identical counts, windows and MS2-to-MS1 map
peaks	249,976,110 MS2	every peak's m/z identical; intensities identical except 2 tied peaks at one m/z in swapped order
time and disk	convert 81 s (before the parallel decode), no mzML	conversion 787 s under mono plus a 3.6 GB mzML, then convert 20 s
six-file HYE experiment, peptides at 1%	159,740	159,525 (within NN seed noise)

The spectra of all six runs were compared one by one, with the same result. The parallel decode is byte-identical to the one-thread decode on a 5 min file. Its timing on the 15 min file will follow once the test host is free.

Requirements and limits

• A .NET 8 runtime on the machine that runs the search (DOTNET_ROOT when it is not in the default location).
• Windows builds need RUSTFLAGS="-C target-feature=+crt-static", because the downloaded .NET host library uses the static C runtime.
• Linux needs a glibc build; the static musl target cannot host .NET.
• Thermo's RawFileReader licence applies to whoever builds or uses it. Nothing MuMDIA ships enables the feature.

Checks

• clippy, with and without the feature, is clean.
• Workspace tests and rustdoc pass, and the config reference is regenerated.
• CI gains a lint step for the feature, so it cannot rot unnoticed.

🤖 Generated with Claude Code