v1.5.0 release candidate 1

• Added loading of sequences from mmCIF files, for ModelAngelo (#207, #217)
• Added loading of sequences from Peaks 11 and Peaks Ab
• Added loading of sequences from Casanovo, pNovo, and MaxNovo (#192)
• Added loading of spectra from Casanovo, pNovo, and MaxNovo (#195)
• Added I/L disambiguation based on satellite ions (#193, #216, #218)
• Added more customization options for peptide fragmentation
• Added hash for all used files in the HTML report (#229)
• Added the option to call parts of a batchfile from another file (include!(<path>)) see the examples (#111, #209)
• Updated the main overview header (#212)
• Updated the command line interface (CLI) to be more friendly, Note: calling stitch has changed to stitch run <path>
• Updated the batchfile parsing to provide more helpful error messages
• Updated the segment overview tree, always use Blosum62, ability to not generate it (BuildTree: False) (#213)
• Updated the exact scoring of reads to handle longer alignments better, as well as locally enforcing unique placement (#215)
• Updated segment joining to use the same alignment as template matching (#128)
• Deprecated the use of booleans with EnforceUnique, for now will keep working with a warning but support will be dropped at some point.
• Fixed small remaining intensity [1-2] scaling for Novor reads to scale [0-1]
• Fixed issues with the generation of the consensus sequences in relation to the mass alignment and I/L disambiguation (#220)
• Fixed leading insertions in reads placement displayed in a different colour, for more clarity in the alignment
• Fixed bugs (#222, #230)
• Performance improvements
• Many more small fixes and improvements

Note

• The benchmarks show a mostly very slightly positive result, with the caveat that I/L disambiguation is not automatically benchmarked yet because raw files are so big.
• Performance has been improved with a couple of tiny steps. The I/L disambiguation though adds extra work and so results in longer runs when used, but this scaling is linear with the number of input reads. The move to net7.0 also gives a bit of performance improvement.

Breaking changes

• The CLI has changed: stitch <batchfile> has been changed to stitch run <batchfile> to better group the applicable arguments for all subcommands. You can use --help to get general help or <subcommand> --help to get help on that subcommand.
• The CSV export has been altered by adding more columns with I/L disambiguation specific information. The order of the other columns has not been changed.

Known issues

• The segment annotation can be off by a couple of aminoacids, or it can miss segments after CDR3.