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smith-chem-wisc / mzLib

Library for mass spectrometry projects
GNU Lesser General Public License v3.0
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Fragger Result reading #770

Closed nbollis closed 6 months ago

nbollis commented 7 months ago

Added classes to readers for MsFragger Psm, Protein, and Peptide reading.

The protein and peptide files have two possible formats. One for the individual file result and one for the combined results. The individual file format is more verbose and has additional fields. the PeptideFile and ProteinFile can be used for either result.

codecov[bot] commented 7 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 75.14%. Comparing base (cf854ac) to head (da79acf). Report is 1 commits behind head on master.

:exclamation: Current head da79acf differs from pull request most recent head b2e83b6. Consider uploading reports for the commit b2e83b6 to get more accurate results

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/770/graphs/tree.svg?width=650&height=150&src=pr&token=1lXMC2BqYG&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/mzLib/pull/770?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 #770 +/- ## ========================================== + Coverage 75.06% 75.14% +0.07% ========================================== Files 189 191 +2 Lines 30235 30307 +72 Branches 3035 3042 +7 ========================================== + Hits 22697 22773 +76 + Misses 7024 7022 -2 + Partials 514 512 -2 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/770?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 | | |---|---|---| | [...nalResults/IndividualResultRecords/MsFraggerPsm.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/770?src=pr&el=tree&filepath=mzLib%2FReaders%2FExternalResults%2FIndividualResultRecords%2FMsFraggerPsm.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9FeHRlcm5hbFJlc3VsdHMvSW5kaXZpZHVhbFJlc3VsdFJlY29yZHMvTXNGcmFnZ2VyUHNtLmNz) | `100.00% <100.00%> (ø)` | | | [...rs/ExternalResults/ResultFiles/MsFraggerPsmFile.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/770?src=pr&el=tree&filepath=mzLib%2FReaders%2FExternalResults%2FResultFiles%2FMsFraggerPsmFile.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9FeHRlcm5hbFJlc3VsdHMvUmVzdWx0RmlsZXMvTXNGcmFnZ2VyUHNtRmlsZS5jcw==) | `100.00% <100.00%> (ø)` | | | [mzLib/Readers/Util/SupportedFileTypes.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/770?src=pr&el=tree&filepath=mzLib%2FReaders%2FUtil%2FSupportedFileTypes.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUmVhZGVycy9VdGlsL1N1cHBvcnRlZEZpbGVUeXBlcy5jcw==) | `100.00% <100.00%> (+7.69%)` | :arrow_up: |