Philosopher 4.6.0

Added

• Added new flag --removecontam to the report command to remove contaminants from the reports
• Added a new combined_psm report to abacus (beta)

Changed

• Updated the TMT-Integrator to match with the version v4.0.0
• Updated the pickedFDR filter
• The pipeline command now accepts annotation files with prefixes
• Updated PTMProphet to the latest release
• Updated the database fetch with the new UniProt API (The new API is still unstable, people might experience hiccups with certain cases, especially non-model organisms without reviewed sequences)

Fixed

• Contaminant tags are now added to Human sequences as well
• Added a fix for errors causes by division-by-zero errors (PR by @chhh)
• Fixed the protein coverage calculations to consider all peptides
• Several minor fixes and updates