Optimize raw file reading for CE calibration only

[picciama]

Is your feature request related to a problem? Please describe.

Currently, we only take the 1000 top scoring target PSMs for CE calibration. Converting an entire RAW file to mzML is therefore not necessary. As such, we should use the query subcommand from ThermoRawFileParser to reduce computation and optimize IO.

Describe the solution you would like

If the user only requests CE calibration, do not convert to mzML but query the required spectra. When doing rescoring, check if mzML exists, and convert if necessary.