RELEASE_NOTES.md

0.2.1 (Released 2026-08-30)

• SparsePeakArray: new module upstreamed from ProteomIQon (sparse binned peak vectors over PeakArray with dot product)
• SearchDB: add Sequence+GlobalMod ModSequence lookup upstreamed from ProteomIQon (prepareSelectModsequenceBySequenceAndGMod, getThreadSafePeptideLookUpFromFileBySequenceAndGMod)
• ProteinInference: adopt the newer ProteomIQon behavior - PSMInput reads the ModelScore column (was PercolatorScore), assignTranscriptsToGenes takes a tryParseProteinID function instead of a regex string, createProteinModelInfoFromEntry reads the GFF3 ID attribute (was Name) and tolerates unknown strand characters as Forward (fixes a runtime match failure), isGene/isRNA generalized over the GFF line type parameter
• FDRControl: add the PEP value machinery upstreamed from ProteomIQon (getLogisticRegressionFunction, createTargetDecoyHis, calculatePEPValues, logitTransformPepValues, initCalculateLin taking a trace callback instead of an NLog logger)

0.2.0 (Released 2026-08-29)

• Upgrade to BioFSharp 2.0.0 (bundles the former BioFSharp.IO package) and migrate the codebase over the breaking API changes
• Align the dependency stack: FSharpAux / FSharpAux.IO 2.1.0, FSharp.Stats 0.6.0, Newtonsoft.Json 13.0.4, Plotly.NET 6.0.0-preview.2
• Replace the legacy FAKE 5 build script with the FAKE 6 build project ported from BioFSharp (build.cmd / build.sh wrappers, GitHub Actions build-test and gh-pages docs deployment, fsdocs 20 documentation pipeline)

0.1.5 - Friday, February 19, 2021

• SignalDetection: add option for peak summation and intensity weighted based mz refinement

0.1.4 - Friday, Oktober 9, 2020

• Minor changes
• SearchDB: added default inclusion of peptides resulting of protein n terminal methionin cleavages.
• FDRControl: added more stable qValue calculation, added storeys qvalue method
• ProteinInference: added FDR calculations

0.1.3 - Monday, March 16, 2020

• Minor changes
• Quantification: improved handling of unsuccessful fits

0.1.2 - Thursday, December 12, 2019

• Minor changes

0.1.1 - Thursday, December 12, 2019

• Minor changes

0.1.0 - Thursday, December 12, 2019

0.0.117 - Friday, September 13, 2019

• include faster hasFlag function
• speed improvements in SequestLike: faster computation of theoretical spectra.

0.0.116 - Saturday, September 7, 2019

• refactor according to changes latest BioFSharp Release

0.0.115 - Friday, September 6, 2019

• add XScoring, a combination of XTandemLike and AndromedaLike Scoring

0.0.114 - Wednesday, September 4, 2019

• add ProteinInference

0.0.113 - Thursday, August 1, 2019

• refactor Fragmentation module according to changes in BioFSharp.Mz release 0.1.1

0.0.112 - Thursday, April 25, 2019

• paket template fix

0.0.111 - Thursday, April 25, 2019

• Initial release

0.0.1 - Thursday, April 25, 2019

• Initial release