feat: native TSV output — bypass mzIdentML for OpenMS/Percolator pipelines

[ypriverol]

Summary

• Add -outputFormat parameter (mzid, tsv, both) to write search results directly to TSV from in-memory objects, bypassing mzIdentML XML serialization + JAXB round-trip
• When -addFeatures 1 is used, 15 Percolator feature columns (ExplainedIonCurrentRatio, NTermIonCurrentRatio, CTermIonCurrentRatio, MS2IonCurrent, NumMatchedMainIons, error statistics) are appended to the TSV
• Peptide modification format (M+15.995) is already compatible with OpenMS MSGFPlusAdapter.modifySequence_() — zero changes needed in OpenMS

Motivation

In quantms/OpenMS, MS-GF+ results flow through:

1. MS-GF+ writes .mzid (JAXB XML serialization)
2. MzIDToTsv reads mzid back via JAXB unmarshaller → .tsv
3. OpenMS MSGFPlusAdapter reads the TSV → idXML

With -outputFormat tsv, steps 1+2 are eliminated entirely. No JAXB object graph, no XML serialization, no multi-GB mzid files.

TSV columns (base)

#SpecFile  SpecID  ScanNum  [Title]  FragMethod  Precursor  IsotopeError
PrecursorError(ppm|Da)  Charge  Peptide  Protein  DeNovoScore  MSGFScore
SpecEValue  EValue  [QValue  PepQValue]

TSV columns (with -addFeatures 1)

All base columns plus:

ExplainedIonCurrentRatio  NTermIonCurrentRatio  CTermIonCurrentRatio
MS2IonCurrent  MS1IonCurrent  IsolationWindowEfficiency
NumMatchedMainIons  MeanErrorAll  StdevErrorAll  MeanErrorTop7
StdevErrorTop7  MeanRelErrorAll  StdevRelErrorAll  MeanRelErrorTop7
StdevRelErrorTop7

Files changed

• New: DirectTSVWriter.java — streams TSV rows from in-memory search results
• Modified: MSGFPlus.java — output format branching after Q-value computation
• Modified: ParamManager.java — new -outputFormat parameter (enum: mzid/tsv/both)
• Modified: SearchParams.java — outputFormat field, writeMzid()/writeTsv() helpers

Verification

• diff between direct TSV and MzIDToTsv output: zero differences (byte-for-byte identical on test.mgf with 818 PSMs)
• All 119 tests pass
• Backwards compatible: default remains mzid

Test plan

• mvn test — 119 tests, 0 failures
• Direct TSV vs MzIDToTsv: identical output verified by diff
• -outputFormat 2 (both): mzid + TSV written correctly
• -addFeatures 1 -outputFormat 1: all 15 Percolator feature columns populated
• Fixed mods (C+57.021), variable mods (M+15.995), MGF Title column all correct
• OpenMS MSGFPlusAdapter: feed TSV, verify idXML output

🤖 Generated with Claude Code

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