Added
- Multi-threading is enabled for `callVariant` to run in parallel.
- CLI command `indexGVF` added to generate a index file for quickly access variant data from the corresponding GVF file. Noted that this command is not required to run.
Changed
- To solve the complexity of subgraphs introduced by fusion and especially alternative splicing insertion and substitution, the `SubgraphTree` class is added to keep the graph-subgraph relationship between nodes.
- Variant records are now kept on disk rather than reading the entire GVF file(s) into memory, and only the file pointers to variant records are kept in memory. This significantly reduces the memory usage of `callVariant`.
- The command line arguments are standardized across all commands, for example '-i/--input-path' for inputs and '-o/--output-path' for outputs.
- `generateIndex` is changed to use compressed text format to store genomic annotation, because for some reason that we are not sure, when loading the pickled genomic annotation, the memory usage is almost doubled. [394](https://github.com/uclahs-cds/package-moPepGen/issues/394)
---