FEAT: updated to timsrust 0.4.0

[sander-willems-bruker]

Updated to timsrust 0.4.0
Major differences:

• Much improved error handling / propagation
• Exposure of parameters for Bruker spectrum reading through the config.json

  "bruker_spectrum_processor": {
    "smoothing_window": 1, 
    "centroiding_window": 1,
    "calibration_tolerance": 0.1,
    "calibrate": false,
    "dia_strategy": {"Quadrupole": {"Even": 1}}
  }

• All parameters should be considered experimental and are use at your own caution. Defaults are generally acceptable, although some settings yield (signifcantly) better or worse results.
• calibrate only is sensible for dda data. Works best if there are many precursors (i.e. long gradient).
• calibration tolerance roughly defines the maximum possible mz difference before/after calibration.
• smoothing_window defines how adjacent tof indices are smoother.
• centroiding_window sets the minimum tof difference between two detections, i.e. relates to TOF resolution in combination with smoothing_window.
• dia_strategy allows to control how dia windows or even frames are translated to DDA-like spectra that are searchable with Sage. Options
  • Quadrupole vs. Window: use the whole frame or just that portion where the quadrupole is not changing
  • None, Even(usize), UniformMobility((f64, f64)), UniformScan((usize, usize)),: The method to split up scans. Even splits its up in an equal partition, whereas the Uniform methods allow finegrained control how many scans are aggregated.

There is room for improvement on how this is implemented on Sage, most is roughly copy-paste at the moment. Feel free to suggest an alternative/better way.

[lazear]

Looks good to me! Could you rebase your branch onto the latest Sage master branch? Looks like there's a conflict in the Cargo.lock files (had to be updated to compile with Rust 1.8.0)

[sander-willems-bruker]

Looks good to me! Could you rebase your branch onto the latest Sage master branch? Looks like there's a conflict in the Cargo.lock files (had to be updated to compile with Rust 1.8.0)

Done!