Use mzdata::mz_read, adding support for gzipped MGF and mzML, and for Thermo raw and mzMLb#1
Merged
Use mzdata::mz_read, adding support for gzipped MGF and mzML, and for Thermo raw and mzMLb#1
mzdata::mz_read, adding support for gzipped MGF and mzML, and for Thermo raw and mzMLb#1Conversation
This add support for gziped files, without the need for us to implement it.
This should add support for gzipped files, MzMLb and Thermo raw files.
This was referenced Aug 23, 2024
The main issue for a fresh build (for some reason I didn't have an issue locally before removing my target directory) seems to be mzpeaks, but there is little reason not to update both.
RalfG
requested changes
Aug 28, 2024
Note that this feauture needs to be called thermorawfilereader. mzdata's feature is called thermo, but the checks, including the one in the `mz_read` macro tests for thermorawfilereader. The feature here needs to match the one tested for in the macro, otherwise rawfiles are detected as a file type, but the macro still wouldn't support it.
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This leaves us with 1 test failure: in our test MGF, PEPMASS is preceded by CHARGE. mzdata now parses the charge, but implicitly assumes there is a PEPMASS first. When that isn't the case, there is no precursor ion to assign the charge value to, resulting in a failure of our unit test.
Work around the bug in mzdata for now, but it might be interesting to, once we upgrade the version of mzdata, to add a test for this.
RalfG
approved these changes
Oct 24, 2024
mzdata::mz_read, adding support for gzipped MGF and mzML, and for Thermo raw and mzMLb
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Use
mzdata::mz_readto read non-bruker files, and adapting the filetype logic accordingly. This adds support for gzipped MGFs and MzMLs, and (untested) for raw files and MzMLb.