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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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[WIP] Reworking PEP to prevent cross-contamination #2390

Closed Alexander-Sol closed 3 months ago

Alexander-Sol commented 4 months ago

This PR builds off the work done in the PR #2387

codecov[bot] commented 4 months ago

Codecov Report

Attention: Patch coverage is 92.76986% with 71 lines in your changes missing coverage. Please review.

Project coverage is 92.75%. Comparing base (7dab370) to head (f20ba24).

Files Patch % Lines
...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs 90.86% 21 Missing and 13 partials :warning:
...pheus/EngineLayer/FdrAnalysis/PeptideMatchGroup.cs 61.76% 13 Missing :warning:
...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs 97.80% 2 Missing and 5 partials :warning:
...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs 95.08% 2 Missing and 4 partials :warning:
...cificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs 42.85% 3 Missing and 1 partial :warning:
MetaMorpheus/TaskLayer/FilteredPsms.cs 89.65% 3 Missing :warning:
MetaMorpheus/TaskLayer/MetaMorpheusTask.cs 96.49% 1 Missing and 1 partial :warning:
...neLayer/ProteinParsimony/ProteinParsimonyEngine.cs 66.66% 0 Missing and 1 partial :warning:
...us/TaskLayer/MbrAnalysis/SpectralRecoveryRunner.cs 93.75% 1 Missing :warning:
Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390/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/2390?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 #2390 +/- ## ========================================== - Coverage 92.97% 92.75% -0.22% ========================================== Files 139 141 +2 Lines 21668 21781 +113 Branches 2983 2984 +1 ========================================== + Hits 20146 20204 +58 - Misses 1043 1099 +56 + Partials 479 478 -1 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...s/EngineLayer/ClassicSearch/ClassicSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FClassicSearch%2FClassicSearchEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NsYXNzaWNTZWFyY2gvQ2xhc3NpY1NlYXJjaEVuZ2luZS5jcw==) | `97.84% <100.00%> (ø)` | | | [MetaMorpheus/EngineLayer/CommonParameters.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FCommonParameters.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NvbW1vblBhcmFtZXRlcnMuY3M=) | `95.67% <100.00%> (+0.08%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmTsvWriter.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmTsvWriter.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Uc3ZXcml0ZXIuY3M=) | `97.54% <100.00%> (ø)` | | | [MetaMorpheus/EngineLayer/SpectralMatch.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FSpectralMatch.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1NwZWN0cmFsTWF0Y2guY3M=) | `97.82% <100.00%> (-1.91%)` | :arrow_down: | | [MetaMorpheus/TaskLayer/MyTaskResults.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FMyTaskResults.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9NeVRhc2tSZXN1bHRzLmNz) | `100.00% <ø> (ø)` | | | [...neLayer/ProteinParsimony/ProteinParsimonyEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FProteinParsimony%2FProteinParsimonyEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1Byb3RlaW5QYXJzaW1vbnkvUHJvdGVpblBhcnNpbW9ueUVuZ2luZS5jcw==) | `98.83% <66.66%> (-0.01%)` | :arrow_down: | | [...us/TaskLayer/MbrAnalysis/SpectralRecoveryRunner.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FMbrAnalysis%2FSpectralRecoveryRunner.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9NYnJBbmFseXNpcy9TcGVjdHJhbFJlY292ZXJ5UnVubmVyLmNz) | `79.08% <93.75%> (-12.39%)` | :arrow_down: | | [MetaMorpheus/TaskLayer/MetaMorpheusTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FMetaMorpheusTask.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9NZXRhTW9ycGhldXNUYXNrLmNz) | `89.09% <96.49%> (+0.59%)` | :arrow_up: | | [MetaMorpheus/TaskLayer/FilteredPsms.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FFilteredPsms.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9GaWx0ZXJlZFBzbXMuY3M=) | `89.65% <89.65%> (ø)` | | | [...cificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FNonSpecificEnzymeSearch%2FNonSpecificEnzymeSearchEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL05vblNwZWNpZmljRW56eW1lU2VhcmNoL05vblNwZWNpZmljRW56eW1lU2VhcmNoRW5naW5lLmNz) | `87.47% <42.85%> (ø)` | | | ... and [4 more](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2390/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)
Alexander-Sol commented 3 months ago

Moved to #2394