Mopepgen

Fixed

- Fixed `VariantPeptideIdentifier` that ORF ID was added before variant IDs.

- Fixed `callVariant` that failed on small circRNA with a lot of variants at the step that creates the cleavage graph. 885

- Fixed `fuzzTest`. Parameters missing for `callVariant`.

Changed

- Changed variant IDs for circRNAs to use backsplicing site instead of listing all exons/introns. 878

- Fixed `splitFasta` that NovelORF peptides coding transcripts not recognized correctly.

- Fixed `VariantPepidePool` that old versions of `SeqUtils.molecular_weight` don't handle `SeqRecord` objects. 874

- `--coding-novel-orf` added to `callNoncoding` and `callVariant` to call novel ORF peptides from coding transcripts. 659

- Renamed `callNoncoding` to `callNovelORF` and replaced the internal source type `Noncoding` to `NovelORF`. 863

Added:

- Flag `--backsplicing-only` added to `callVariant` to allow only calling noncanonical peptides spanning backsplicing site from circRNA events. 858

Fixed:

- Adjacent variants were not merged as MNVs successfully. The function always exited with nothing.

- Because of the updating to on-disk GTF, the coding transcripts were not generated and saved successfully. `filterFasta` is the only command affected.

- Updated `splitFasta` and `summarizeFasta` to accept source combinations in `--order-source`.

- Fixed `parseCIRCexplorer` so the exon/intron indices in variant IDs are sorted correctly.

- Fixed `parseVEP` to handle insertions in start-inclusion. 840

- Fixed `callVariant` of 'no reference out node found'. 842

- Fixed `mergeFasta` to remove redundant FASTA header entries. 846

- Fixed `GenomicAnnotation` to parse ENSEMBL style UTR correctly. 687

- Switch to use python's `logging` package for logging.

- Print basic summary to `callVariant` output. 412

Add

- Added `--timeout-seconds` to callVariant.

- Added `metadata.json` to the index directory for all essential parameters of how a moPepGen index directory is created, including cleavage parameters. 850

- Added `updateIndex` 853

- Output a peptide table for additional information. 833