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Changes to PEP Calculation and Filtering #2387

Merged
merged 56 commits into from
Aug 5, 2024
Merged

Changes to PEP Calculation and Filtering #2387

merged 56 commits into from
Aug 5, 2024

Commits on Jun 18, 2024

  1. new style computation of pep q-value

    @trishorts
    trishorts committed Jun 18, 2024
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  2. fixed unit tests

    @trishorts
    trishorts committed Jun 18, 2024
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Commits on Jun 19, 2024

  1. separate PsmFdrInfo and PeptideFdrInfo calculations in FdrAnalysisEngine

    @trishorts
    trishorts committed Jun 19, 2024
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  2. d

    @trishorts
    trishorts committed Jun 19, 2024
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  3. fdh

    @trishorts
    trishorts committed Jun 19, 2024
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Commits on Jun 25, 2024

  1. not working yet

    @trishorts
    trishorts committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. maybe better maybe not

    @trishorts
    trishorts committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. huh

    @trishorts
    trishorts committed Jun 27, 2024
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Commits on Jul 1, 2024

  1. tr

    @trishorts
    trishorts committed Jul 1, 2024
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Commits on Jul 3, 2024

  1. j

    @trishorts
    trishorts committed Jul 3, 2024
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  2. 53

    @trishorts
    trishorts committed Jul 3, 2024
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Commits on Jul 17, 2024

  1. Fixed filtering kinda

    @Alexander-Sol
    Alexander-Sol committed Jul 17, 2024
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  2. commit before i start breaking things

    @Alexander-Sol
    Alexander-Sol committed Jul 17, 2024
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  3. still sorta broken

    @Alexander-Sol
    Alexander-Sol committed Jul 17, 2024
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  4. idk

    @Alexander-Sol
    Alexander-Sol committed Jul 17, 2024
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  5. Fixed most issues, moved filtering to MetaMorpheus Task

    @Alexander-Sol
    Alexander-Sol committed Jul 17, 2024
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Commits on Jul 18, 2024

  1. fix multiprotease unit test

    @trishorts
    trishorts committed Jul 18, 2024
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  2. fix MakeSureFdrDoesntSkip

    @trishorts
    trishorts committed Jul 18, 2024
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  3. fix TestPeptideCount

    @trishorts
    trishorts committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. new postsearchanalysistask results generator

    @trishorts
    trishorts committed Jul 19, 2024
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  2. fixed results output in postsearchanalysistask

    @trishorts
    trishorts committed Jul 19, 2024
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  3. yert

    @trishorts
    trishorts committed Jul 19, 2024
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Commits on Jul 22, 2024

  1. fix pep q-value calc

    @trishorts
    trishorts committed Jul 22, 2024
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  2. fix peptideFdrTest

    @trishorts
    trishorts committed Jul 22, 2024
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  3. fix spectral recovery

    @trishorts
    trishorts committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. ity

    @trishorts
    trishorts committed Jul 23, 2024
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  2. fix semi specific test

    @trishorts
    trishorts committed Jul 23, 2024
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  3. fix metadraw test

    @trishorts
    trishorts committed Jul 23, 2024
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  4. lkah

    @trishorts
    trishorts committed Jul 23, 2024
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  5. poiu

    @trishorts
    trishorts committed Jul 23, 2024
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  6. slice test fixed

    @trishorts
    trishorts committed Jul 23, 2024
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  7. merge upstream

    @trishorts
    trishorts committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. some tests

    @trishorts
    trishorts committed Jul 24, 2024
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  2. some testst

    @trishorts
    trishorts committed Jul 24, 2024
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  3. fixed most of silac unit tests

    @trishorts
    trishorts committed Jul 24, 2024
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  4. hmm

    @trishorts
    trishorts committed Jul 24, 2024
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  5. dsg

    @trishorts
    trishorts committed Jul 24, 2024
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  6. uio

    @trishorts
    trishorts committed Jul 24, 2024
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  7. kjg

    @trishorts
    trishorts committed Jul 24, 2024
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  8. ghk

    @trishorts
    trishorts committed Jul 24, 2024
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  9. Fixed the few remaining tests that were breaking

    @Alexander-Sol
    Alexander-Sol committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. Five tests breaking, mostly numbers

    @Alexander-Sol
    Alexander-Sol committed Jul 25, 2024
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  2. Fixed results.txt writer for PEP-Q-values.

    @Alexander-Sol
    Alexander-Sol committed Jul 25, 2024
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  3. Fixed output bug

    @Alexander-Sol
    Alexander-Sol committed Jul 25, 2024
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  4. idk

    @Alexander-Sol
    Alexander-Sol committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. broken

    @Alexander-Sol
    Alexander-Sol committed Jul 26, 2024
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  2. Finally fixed!!!

    @Alexander-Sol
    Alexander-Sol committed Jul 26, 2024
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Commits on Jul 29, 2024

  1. Merge branch 'master' into ShortreedPep3

    @Alexander-Sol
    Alexander-Sol authored Jul 29, 2024
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  2. Added QValueThresholdForPEP to common params

    @Alexander-Sol
    Alexander-Sol committed Jul 29, 2024
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Commits on Jul 31, 2024

  1. Addressed Nic's comments

    @Alexander-Sol
    Alexander-Sol committed Jul 31, 2024
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  2. Fixed tests that broke when addressing Nic's comments

    @Alexander-Sol
    Alexander-Sol committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Made fields in FilteredPsms more explicit

    @Alexander-Sol
    Alexander-Sol committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. added comments - MRS

    @Alexander-Sol
    Alexander-Sol committed Aug 2, 2024
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  2. More comments, better ordering

    @Alexander-Sol
    Alexander-Sol committed Aug 2, 2024
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  3. Merge branch 'master' into ShortreedPep3

    @trishorts
    trishorts authored Aug 2, 2024
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  4. Merge branch 'master' into ShortreedPep3

    @trishorts
    trishorts authored Aug 2, 2024
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