Msstitch

Added
- Add PEP (posterior error) from percolator to output
- Possible to do median-centering on a peptide/protein/gene table using median factors from another table (e.g. PTM peptides centered with a protein table)

Changed
- No longer recalculate percolator FDR to avoid mix-max, let user choose in percolator instead

Fixed
- Genecentric peptide table merging bug with many identical gene output fixed

Changed
- Field order in peptide/protein tables: channels of all sets, then of PSMs used to quantify

Fixed
- Deletesets bug where unused peptide sequences where not removed from DB due to a missing commit
- Fix percolator to TSV ID creation which affected non-scannumbered data (e.g. TIMS data) where multiple PSMs to spectrum occur and it keeps enumerating scans

Fixed
- Peptide table merge bug that piled on duplicate proteins and exploded in processing time at big datasets

Added
- Total protein normalization of PTM peptides
- PTM FLR stored and output in peptide table merges
- Precursor ion fraction (purity) from OpenMS to PSM table
- Precursor purity filter sets PSM quant to NA, keeps PSMs

Fixed
- Do not create duplicate isobaric channels in DB and with that in PSM output
- Do not add standard fields to PSM refined header that are already there
- Do not crash on peptide table merge when a peptide has e.g. 600 protein matches
- Merging no-group peptide tables no longer output multiple identical protein accessions for a peptide
- Peptide table genecentric merge gets all genes per peptide, not only one

Changed
- Isobaric quant summarizing to features now throws out all PSMs with NA in a channel by default, keep them with --keep-psms-na-quant

Added
- Isobaric quant summarizing using denominators OR sweep OR median intensity
- Median normalization possible for isobaric quant
- Column in results "number of fully quanted PSMs", i.e. without missing values
- `msstitch deleteset` can delete a sample set from PSM tables and sqlite lookups
- `msstitch psmtable` can take `--oldpsms` to append new PSMs to an existing table (with identical search etc)

Fixed
- Bug (and free speed increase) where merged tables the following fields would be all wrong and all the same for each set: amount PSMs, amount peptides, amount unique peptides
- MS1 quant bug where sometimes wrong features where fetched to align to a scan