Version 0.2

This fixes a bug where in mzML it is possible to have referenceableParamGroupList that provide ms level for spectra and that was not read.

Initial release

Initial release of the generate spectrum index script.

This is a script to read spectrum peak files and output the nativeID, MS-level, and MS2+ index (defined as the 0-based index for all spectra of MS-level 2 and higher) for each spectrum. Supported input types are mzML, mzML.gz, mzXML, and mgf.

A note on the nativeID column. For mzML and mzML.gz the nativeID is read directly, for mzXML it is constructed as a scan=, and for mgf it is constructed as scan= IF there is a SCANS= field in the MGF, otherwise it is constructed as index= and is the 0-based index of all spectra in the file.