Mopepgen

Fixed

- Noncoding peptide headers not parsed successfully by summarizeFasta 672

Fixed

- Fixed `callVariant` that alt splice insertions were treated as stop altering when they are not.

- Argument `--orf-assignment` added to `callNoncoding` to allow choosing the min or max ORF. 667

Fixed

- When filtering variants for circRNA, those on fragments that are shorter than 3 nucleotides will not be included. 613

- When collapsing nodes with the same sequence, global variants (mostly circRNA) are no longer considered when comparing variants, so that nodes with no other variant won't be discarded mistakenly. 619

- Fixed issue that for hybrid nodes that span over a junction site on a circRNA, the location got lost and caused it to fail to identify whether the node is at least one loop downstream to an ORF start site. 621

- Fixed issue that circRNA with only 1 nucleotide was causing it to fail to filter variants. 623

- Fixed issue that peptide nodes on different subgraphs were collapsed after expanding the variant bubble, causing downstream nodes to be unprocessed and resulting in `*` in the final sequences. 625

- Fixed issue that the ORF start site position cannot be interpreted when checking whether it is at least one loop away, because it can be off by 1 when converting the location from the gene coordinate to amino acid. 630

- Fixed issue that the 'CHROM' attribute of GVF metadata not read in correctly. 629

- Fixed issue that when a frameshift insertion is on a alt splice frameshift substitution (or insertion), the node became disconnected after aligning the variant bubble. 635

- Fixed issue that when getting the stop altering mutations, location comparison was done incorrectly by 1. 636

- Node in circRNA missing downstream stop lost mutation called as variant peptide incorrectly. 637

- Silent mutation not excluded when it is very closed to anther mutation. 638

- Stop retaining mutation not excluded. 638

- Fusion with donor breakpoint smaller than 3 causing it fail to run. 633

- Alt splice insertion recognized as stop altering incorrectly. 640

- Fix that variants that overlap with last 3 nucleotides of the transcripts causing it to fail. 645

- Fixed `parseREDItools` that the ref and alt nucleotides were not set correctly for negative strands. 644

- Fixed `callVariant` that hybrid peptide sequences were called from circRNA. 653

- Fixed `callVariant` that peptides with variants of in-frame mutation causing deletion/insertion between two cleavage sites were missed. 655

- Fixed `callVariant` that when setting the max number of variants per peptide, the number of miscleavages was not used correctly. 657

Changed

- The transcript trailing peptides (peptides at the end of the transcript sequence) are now excluded for transcripts with the `mRNA_end_NF` tag and circRNA regardless of it. Otherwise for transcripts (either coding or noncoding) that the mRNA end is confirmed (without the `mRNA_end_NF`) they are now included in the final FASTA. 649

- Change from ray back to pathos for parallelization. 643

- Gene ID of the transcript from which a noncoding peptide is called is added to the FASTA header. 662

Fixed

- Transcriptional coordinate to genomic coordinate not converted successfully when it is the last nucleotide of the transcript. 592

- When creating the peptide cleavage graph, the end nodes of ate variant bubble with alt splice were collapsed with the reference node causing the graph cleavage process terminated too early resulting uncleaved nodes. 597

- in `callVariant` when filtering variants associated with the donor transcript, the left breakpoint coordinate not converted successfully if it is the end of the transcript. 598

- Large deletion caused by alt splice raised the complexity drastically so had to go back to treat alt splice deletion as subgraph again. 600

- In circRNA, nodes that span over the backsplicing site with variant before the backsplicing site were not recognized correctly. 602

- Failed to find the downstream exon start when the breakpoint is the first nucleotide before the exon start of a transcript on the negative strand. 603

- In `bruteForce`, variants that start at the fusion breakpoint were not excluded. 604

- Variant peptides on circRNA are missed by `callVariant` when there are multiple ORF candidates. 606

Added

- Added support for fusion, alternative splicing and circRNA in `bruteForce`.

Fixed

- Several issues of `bruteForce` were fixed for fusion, alternative splicing and circRNA to be consistent with `callVariant`.

- In `ThreeFrameTVG` and `PeptideVariantGraph`, large deletions (for alternative splicing) are no longer treated as subgraphs any more.

- Fixed the issue that the `subgraph_id` attributes of `TVGNode` and `PVGNode` are lost after nodes are merged. 566

- When expanding the aligned variant bubble, if the downstream node of the start node has multiple inbond nodes, nucleotides will be taken from the downstream node and added to each upstreams

- Fixed `callVariant` that when filtering variants that are compatible with fusion, the breakpoint site were not recognized correctly. 567

- For `ThreeFrameTVG', when aligning variant bubbles, if the end of the first variant is the start of the next (e.g. alternative splicing events that sharing the same splicing site), the merged bubble will then contain both variants

- Fixed `callVariant` that mutations are assigned as stop altering mutation when there is a start codon after it. 568

- Fixed `callVariant` that alternative splicing variants were not recognized as stop altering mutation correctly because their reference sequence from GVF is only the first nucleotide. 569

- Fixed `callVariant` that nodes being lost after an in-frame subgraph. 573

- Fixed `callVariant` that the actual fusion breakpoint was not found correctly when trying to tell whether a novel start site should be considered.

- Fixed `callVariant` that variant peptides were called with variants present in one loop but not in another. 576

- When collapsing the end nodes when creating the peptide cleavage graph, nodes that contains alt splice deletions are now separated from others. 580

- Fusion not inserted correctly when the breakpoint is intronic. 578

- When finding start altering variants from a node, wrong right position was used. 583

Fixed

- Fixed issue of alternative splicing deletion that starts at the third nucleotide of start codon. Those variants are now skipped. 560