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wkumler / RaMS

R-based access to Mass-Spectrometry data
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Fix for negative mzML, checks time unit, and small update of .gitignore for a dev folder #12

Closed ricardo-cunha closed 1 year ago

ricardo-cunha commented 1 year ago

Hi William,

I added a small fix for parsing negative polarity in mzML files, as the accession code is different. I checked negative mzXML and works fine. Also, included an option to check the actual time unit in both mzML and mzXML instead of guessing from the duration of the run. What you think?

Cheers, Ricardo

codecov-commenter commented 1 year ago

Codecov Report

Base: 85.41% // Head: 85.50% // Increases project coverage by +0.09% :tada:

Coverage data is based on head (02065b9) compared to base (d4c4d98). Patch coverage: 94.11% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #12 +/- ## ========================================== + Coverage 85.41% 85.50% +0.09% ========================================== Files 5 5 Lines 1083 1090 +7 ========================================== + Hits 925 932 +7 Misses 158 158 ``` | [Impacted Files](https://codecov.io/gh/wkumler/RaMS/pull/12?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=William) | Coverage Δ | | |---|---|---| | [R/grabMzmlFunctions.R](https://codecov.io/gh/wkumler/RaMS/pull/12/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=William#diff-Ui9ncmFiTXptbEZ1bmN0aW9ucy5S) | `86.59% <92.30%> (+0.26%)` | :arrow_up: | | [R/grabMzxmlFunctions.R](https://codecov.io/gh/wkumler/RaMS/pull/12/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=William#diff-Ui9ncmFiTXp4bWxGdW5jdGlvbnMuUg==) | `87.04% <100.00%> (+0.13%)` | :arrow_up: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=William). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=William)

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wkumler commented 1 year ago

Nice catch! Thanks for the PR - I've built these recommendations into v1.3 and will push them to master once a question about the DAD formatting is resolved.