CHANGELOG

v0.6.1
- Fix missing tmt_ms_level argument for tmt_requantify

v0.6.0
- Add cache folder option to reuse previously generated results from a different SIMSI run (#27)
- Memory and runtime optimizations (#26)
- Hotfix for NaN handling in evidence assembly
- Added "Potential contaminant" column in SIMSI output based on the "Proteins" column
- Added sorting step to prevent rare event of incorrect probability strings
- Added validation option for mzml conversion
- Improved raw file converter interface
- Removing importlib dependency from poetry
- Improved SIMSI version retrieval for logger
- Added sorting of raw files to prevent downstream problems

v0.5.0
- New GUI! Now it supports all parameters usually needed
- Added optional filter for maximum Posterior Error Probability considered for transfers

v0.4.8
- Fixed MaRaCluster .dat file handling

v0.4.7
- Fixed TMT6plex handling; now takes correct masses

v0.4.6
- Fixed .exe building

v0.4.5
- Updated MaRaCluster to v1.03

v0.4.4
- Added automatic .exe building upon release

v0.4.3
- Fixed metafile handling with multiple reporter ion files again

v0.4.2
- Fixed metafile handling with multiple reporter ion files

v0.4.1
- Support for TMT-Pro and other isobaric labels
- Added TMT correction factor files to meta file input

v0.4.0
- Added support for a meta file with multiple raw and MQ input folders
- Updated ThermoRawFileParser to v1.4.0, fixes wrong MS3->MS2 assignment issue
- Added support for majority vote for PTM-ambiguous clusters
- Added calculation of average phospho-probability string
- Added support for keeping the decoy hits from the MQ output (enabled by default)

v0.3.2
- Updated MaRaCluster to v1.02

v0.3.1
- Improved handling of missing columns in evidence.txt and msms.txt input files
- Improved logging
- Added greeter and README badges

v0.3.0
- Fixed issue with MS1 feature assignment for transferred identifications
- Made naming of evidence output file consistent (.txt instead of .csv)
- Improved log messages for statistics and evidence building

v0.2.2
- Fixed problem with multiprocessing on Linux with more than 80 files

v0.2.1
- Minor bug fixes for Windows GUI
- Fill Experiment column with constant value if missing

v0.2.0
- Fixed support for ambiguous localization of phosphorylation sites
- Fix for Pandas 1.4: changed df.append to pd.concat
- Added automatic writing of log file to output folder
- Multithreading for TMT extraction
- Major refactoring
- Fixed double printing in multithreading
- Added column with all sequences in the transferred cluster
- Capped default number of threads to 4

v0.1.0
- Initial release