Mopepgen

Changed

- Fixed `callVariant` that it failed when the breakpoint of a fusion is right at the end of the start codon because it tried convert to end inclusion. 454

- Fixed `callVariant` that no variant peptides are called when the first variant is a fusion. 454

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Changed

- A warning is raised in `parseVEP` when tryping to parse a MNV (multi-nucleotide variant) and skip the record instead of raising an error. 447

- Fixed `summarizeFasta` that source order of `Noncoding` was not recognized. 449

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Changed

- Fixed the problem that in `summarizeFasta` output the order of variant sources in the same group is not consistent across runs. 428

- Argument `--ignore-missing-source` added to `summarizeFasta` so sources not present in any GVF can be ignored without raising any error. 436

- In `filterFasta`, when filter with expression table, changed to filter out peptides smaller than, instead of smaller or equal to, the value of `--quant-cutoff`.

- Fixed the issue that in `splitFasta`, variant sources are not grouped as they are specified by `--group-source` 439

Added

- Resources usage including memory, CPU and time is now printed to stdout in the end of all command line programs.

Fixed

- Fixed issue that `--additional-split` not recognized properly in `splitFasta`. 443

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Added

- Added CLI command `summarizeFasta` to output a summary table of the variant peptide FASTA file output by `callVariant`.

Changed

- Attribute key for transcript ID is fixed from 'TRANSCRIPT' to 'TRANSCRIPT_ID' in circRNA's GVF files output by `parseCIRCExplorer` to be the same as other GVF files.

- Genomic position for each record is added to the GVF file output by `parseCIRCExplorer`.

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Changed

- Argument parameter `--decoy_string_position` is changed to `--decoy-string-position`. 417

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Added

- Enable `filterFasta` to filter by number of miscleavages per peptide. 382

- Added CLI command `mergeFasta` to merge multiple variant peptide database Fasta files into one. This could be useful when working with multiplexed proteomic experiments such as TMT. [380](https://github.com/uclahs-cds/package-moPepGen/issues/380)

- Added CLI command `decoyFasta` to generate decoy database by shuffling or reversing each sequence. [386](https://github.com/uclahs-cds/package-moPepGen/issues/386)

- Added parameter `--min-coverage-rna` to `parseREDItools` to filter by total RNA reads at a given position. 392

- Added CLI command `encodeFasta` to replace the variant peptide headers with UUIDs. The original FASTA headers are stored in a text file together with the UUIDs. This is to make the FASTA header short enough for library search engines. 389

Changed

- Donor and accepter transcript IDs are now explicitly included in the variant IDs of fusion in both GVFs and variaint peptide FASTA headers. Closed 376 via 377

- For fusion, `callVariant` now looks at the entire accepter sequence for potential variant peptides, rather than only the peptides that contains the breakpoint. 377

- `filterFasta` updated to support filter by number of miscleavages. 383

- In `parseVEP`, chromosome seqname for each record is now read directly from the gene annotation, to avoid the 'chr' prefix issue. 391

- The `--transcript-id-column` parameter of `parseREDItools` is changed to take 1-based index. 392

- Changed `splitDatabase` to `splitFasta` for consistency. 397

- Updated `generateIndex` to reduce the size of genomic annotation data and the memory usage when loaded. 395

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