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