fix(#157): preserve PSM scores when DeNovoScore is below threshold#4
Merged
ypriverol merged 3 commits intofix/test-infrastructurefrom Apr 13, 2026
Merged
Conversation
…shold In MZIdentMLGen.addSpectrumIdentificationResults(), change `break` to `continue` when a match has DeNovoScore below the minimum threshold. The `break` was incorrectly stopping emission of all subsequent matches for that spectrum, silently dropping valid PSMs from the mzid output. Also add null safety check for spectrum index lookup — if a spectrum index is not found in the spectrum file, log a warning and skip instead of throwing a NullPointerException. Add TestMZIdentMLGen with two integration tests: - testMzidScoreCompleteness: runs MSGF+ search, verifies every SII has all 4 score CVParams (RawScore, DeNovoScore, SpecEValue, EValue) - testMzidStructuralValidity: verifies output mzid has required mzIdentML structure elements Closes MSGFPlus#157 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add new -msLevel CLI parameter to filter spectra by MS level. Accepts single value (e.g., -msLevel 2) or comma-separated range (e.g., -msLevel 2,3). Default is 2 (MS2 only). Changes: - ParamManager: add MS_LEVEL enum and registration - IntRangeParameter: enable single-value parsing, fix typo - SearchParams: add minMSLevel/maxMSLevel fields - SpecKey: filter spectra by MS level in getSpecKeyList() - SpectraAccessor: add setMSLevelRange(), wire to parsers - MzMLAdapter/MzXMLSpectraMap: fix maxMSLevel to be inclusive - MSGFPlus/MSGFDB/MSGFDBLib: wire MS level parameters - pom.xml: remove fastutil shade filter (jmzml 1.7.11 needs full fastutil) Tests: TestIntRangeParameter (9 tests), TestMSLevelFiltering (6 tests) Benchmark (TMT 1.1GB, TDA): Baseline: 1245s, 6654 PSMs@1%FDR -msLevel 2: 957s (-23%), 6936 PSMs@1%FDR (+4.2%) Closes MSGFPlus#159 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
|
Important Review skippedAuto reviews are disabled on base/target branches other than the default branch. Please check the settings in the CodeRabbit UI or the ⚙️ Run configurationConfiguration used: defaults Review profile: CHILL Plan: Pro Run ID: You can disable this status message by setting the Use the checkbox below for a quick retry:
✨ Finishing Touches🧪 Generate unit tests (beta)
Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out. Comment |
feat(MSGFPlus#159): add -msLevel parameter for MS level filtering
Member
Author
|
Related with issue: MSGFPlus#157 |
4 tasks
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
breaktocontinueinMZIdentMLGen.addSpectrumIdentificationResults()so that PSMs after a low-DeNovoScore match are not silently dropped from the mzid outputFiles Changed
src/main/java/edu/ucsd/msjava/mzid/MZIdentMLGen.java(2 line changes)src/test/java/msgfplus/TestMZIdentMLGen.java(new, 2 integration tests)Benchmark (TMT 1.1GB mzML, target-decoy, 4 threads)
Note: Performance improvement comes from updated jmzml 1.7.11 dependency (PR0), not from this fix.
Test plan
mvn testpasses (122 tests, 0 failures)Closes MSGFPlus#157
🤖 Generated with Claude Code