- Fixed issue that mouse reference genome and proteome were not parsed correctly. 546
- Fixed issue that stop-lost inframe deletions being missed during node collapsing. 549
- Fixed issue that variants missed by callVariant when multiple variants are causing the same sequence. 552
- Fixed issue that `cpop_collapsed` attribute was not retained after merging so peptides that don't end with cleavage sites were yield. 554
- Fixed problem caused by N in the reference DNA sequence. 556
---
0.9.2
Fixed
- For circRNA, each reading frame subgraph is now replicated for 3 times in order to catch all variant peptides that read through the junction site. 514
- For `decoyFasta`, overlapping decoy sequences are also counted and printed to the stdout when using reverse. 474
Added
- Enzyme lysN is added. 523
---
0.9.1
Added
- UTIL command line tool `validateNoncodingCalling` added to validate the output of `callNoncoding` with `bruteForceNoncoding`. 524
Fixed
- `parseVEP` updated to only parse the first 13 columns of the VEP TSV. 540
---
0.9.0
Fixed
- Fixed issue that peptides caused by start gain mutations are not called by `bruteForce`. 492
- Fixed issue that variant peptides caused by start gain mutations from noncoding transcripts are not called in some cases. Stop gain mutations from downstream are also missed in some cases. 495
- Fixed issue that some variant peptides were not called with in-frame deletions. 515
- Fixed issue that the shuffled decoy sequences produced by decoyFasta are not reproducible when input FASTA order is changed. 517
- Fixed issue that stop lost mutations are not recognized correctly. 519
- Fixed issue that start gain and stop lost mutations before the novel start site were not excluded. 520
- Fixed issue that frameshifting mutations on the same node of a novel ORF start site and is right after it was not carried over to downstream nodes. 526
- Fixed issue that stop lost mutations were not recognized for deletions. 527
- Fixed issue that in-frame deletion stop retaining mutations were not recognized 528
- Fixed issue that variant coordinates not handled correctly when the cleavage site is contained in the inserted sequence. 52
- Fixed issue that peptides are not called with overlapping deletions. 531
---
0.8.1
Fixed
- The attribute `global_variant` is added to the `PeptideVariantGraph` so for circRNA, if the entire variant peptide is called from an insertion sequence, the variant of circRNA is still going to be added. So the FASTA header will be written out correctly. 490
0.8.0
Fixed
- Fixed issue that variants are not filtered correctly on `ThreeFrameCVG` (some variants are discarded or retained incorrectly). 488