Release 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

Release 0.8.0

Fixed

• Fixed issue that variants are not filtered correctly on ThreeFrameCVG (some variants are discarded or retained incorrectly). #488

Release 0.7.2

Fixed

• Rolled back to not filtering candidate variant peptides that overlaps with canonical peptide pool at transcript level in PeptideVariantGraph because accessing the shared memory object is too slow (which could be optimized in the future).

Release 0.7.1

Changed

• callVariant optimized so the memory usage and run time is reduced to better handle hyper-mutated regions. #483

• Switched from pathos to ray because the latter has better support for shared memory.

Release 0.6.2

Fixed

• Fixed the issue that large insertions, such as retained introns, that start right after the start codon were not converted to end inclusion successfully. #470

Release 0.6.1

Fixed

• Deletion was mistreated as insertion when trying to convert to end-inclusion format. This only affects deletions that start on the third nucleotide of CDS. #468

Release 0.6.0

Fixed

• callVariant very slow on certain cases when the transcript is large. #464

• callVariant failed to find start codon for transcript with fusion being the first variant and the donor breakpoint is intronic. #465

Release 0.5.1

Added

• Option --denylist is added to filterFasta to accept a FASTA file to exclude peptide sequences from it.

Release 0.5.0

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

Release 0.4.2

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