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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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N-glyco search improvements #2322

Closed trishorts closed 7 months ago

trishorts commented 9 months ago

Addition of glyco-quant had previously messed up the N-glycan search. This PR fixes those bugs and properly handles output from O-, N- and ON-glyco combined search allowing quant and creation of individual file results with reporting of the correct motifs.

codecov[bot] commented 9 months ago

Codecov Report

Attention: 11 lines in your changes are missing coverage. Please review.

Comparison is base (da174f0) 92.68% compared to head (de61bf9) 92.67%.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322/graphs/tree.svg?width=650&height=150&src=pr&token=m0HXyK8tFy&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #2322 +/- ## ========================================== - Coverage 92.68% 92.67% -0.02% ========================================== Files 136 137 +1 Lines 21302 21262 -40 Branches 2924 2928 +4 ========================================== - Hits 19744 19704 -40 + Misses 1086 1080 -6 - Partials 472 478 +6 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL0ZkckFuYWx5c2lzRW5naW5lLmNz) | `91.42% <100.00%> (+0.04%)` | :arrow_up: | | [...TaskLayer/XLSearchTask/PostXLSearchAnalysisTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9YTFNlYXJjaFRhc2svUG9zdFhMU2VhcmNoQW5hbHlzaXNUYXNrLmNz) | `79.56% <100.00%> (ø)` | | | [MetaMorpheus/TaskLayer/XLSearchTask/WriteXlFile.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9YTFNlYXJjaFRhc2svV3JpdGVYbEZpbGUuY3M=) | `99.45% <ø> (ø)` | | | [...yer/GlycoSearchTask/PostGlycoSearchAnalysisTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9HbHljb1NlYXJjaFRhc2svUG9zdEdseWNvU2VhcmNoQW5hbHlzaXNUYXNrLmNz) | `94.24% <96.29%> (-0.94%)` | :arrow_down: | | [...heus/EngineLayer/GlycoSearch/GlycoSpectralMatch.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0dseWNvU3BlY3RyYWxNYXRjaC5jcw==) | `94.26% <90.24%> (-1.94%)` | :arrow_down: | | [...rpheus/TaskLayer/GlycoSearchTask/WriteGlycoFile.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9HbHljb1NlYXJjaFRhc2svV3JpdGVHbHljb0ZpbGUuY3M=) | `95.18% <95.18%> (ø)` | | ... and [2 files with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2322/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)