Mopepgen

- `--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

Add

- Added `--graph-output-dir` to save graph data in json.

Fixed

- Fixed `summarizeFasta` that SEC and W2F on fusion peptides are ignored. 789

- Fixed `callVariant` that `variant_coordinates_to_gene` failed when the deletion is end inclusion and it overlaps with the last nucleotide of an exon. 793

- Fixed `splitFasta` that CodonReassign and SECT were not able to be grouped. 796

- Fixed `callVariant` that in-frame subgraphs not recognized when they are not in variant bubble.

- Fixed `callVariant` that peptides are falsely called if the last miscleaved node is missing a downstream cleavage altering variant. 800

- Fixed `TVGNode` that `get_max_subgraph_id` always returns the last subgraph ID. 802

- Fixed `callVariant` with altSplice insertion with intronic frameshift variant which is very closed to the end of the subgraph. 803

- Fixed `bruteForce` that accepter variants are skipped if the donor transcript has variants with the same coordinate. 810

- Fixed `splitFasta` that source and source group order gets overriden by GVF order. 805

- Fixed `summarizeFasta` and `splitFasta` being too slow. 795

- Fixed `splitFasta` to use top priority header for additional split

- Fixed `callVariant` that some accepter only ORFs maybe included for noncoding fusion transcripts.

- Fixed `callVariant` that when filtering variants for a given transcript/fusion/circRNA, coordinates of end inclusion insertions were not interpreted correctly.

- Fixed `bruteForce` that selenocysteine not fixed for deletion alt sequence.

- Fixed `callVariant` that nodes with fusion being treated as subgraph out or end node incorrectly.

- Fixed `callVariant` that upstream cleavage altering variants were affecting checks for whether a node is hybrid in circRNA.

- Fixed `callVariant` that two SNV at the same location in circRNA was affecting hybrid node identification.

- Fixed `callVariant`. When creating the cleavage graph, when a variant bubble is processed, the downstream node(s) needs to be identified for the next iteration, and only in-frame node should be used. However some nodes can span over two reading frames, so we should check the last reading frame index instead of the first.

- Fixed `callVariant` that accepter transcript variants very closed to the breakpoint were skipped.

Added

- Added support for `--group-source` for `summarizeFasta`. 798

Fixed

- Fixed that reference source are not recognized. Switched to use upper case values. 758

- Fixed `generateIndex` that symlink was not created properly for GTF with `--gtf-symlink`.

- Fixed matplotlib warning message 742

- Fixed `parseVEP` that insertions not parsed successfully if the location is a single base. 766

- Fixed `callVariant` that peptides with upstream cleavage altering mutations were not called. 670

- Fixed fuzzTest to take multiple CPUs and use temporary directory.

- Fixed issue in callVariant of circRNA with a SNV being silent in the first loop but not in the second.

- Fixed issue that circRNA peptide nodes with and without a silent mutation were collapsed. 778

- Fixed that circRNA peptides that carry indels incompatible with the orf start node should not be called. 780

- Fixed that hybrid node was not identified if the variant is in the end of an exon. 782

- Fixed that in circRNA, cleavage gain from upstream node is added to the the wrong ORF. 783

- Fixed callVariant that `fit_into_codon` terminated early in fusion transcripts when there donor has a frameshift and accepter has a variant right after the breakpoint. 786

Fixed

- Reduced memory usage by mapping the GTF files into memory instead of reading it all at once. 371