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Use mzdata::mz_read
, adding support for gzipped MGF and mzML, and for Thermo raw and mzMLb
#1
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Commits on Aug 13, 2024
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use mz_read to read mgfs and mzmls
This add support for gziped files, without the need for us to implement it.
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use infer_from_path to determine filetype
This should add support for gzipped files, MzMLb and Thermo raw files.
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Commits on Aug 23, 2024
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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.
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Commits on Aug 29, 2024
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add feature for thermo rawfile support
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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Commits on Sep 18, 2024
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Commits on Sep 23, 2024
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Commits on Oct 23, 2024
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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.
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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.
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