CHANGELOG.md

Changelog

0.17.4 (2024-12-09)

Bug Fixes

• Sec and Stop coincide in SEPHS2 (#214) (8ae7e73)

0.17.3 (2024-10-04)

Bug Fixes

• Add catch-all tag Other to account for future cdot tag changes (#204) (e02c98c)

0.17.2 (2024-08-06)

Bug Fixes

• add support for tag 'GENCODE Primary' in cdot json (#201) (0b37341)

0.17.1 (2024-07-26)

Bug Fixes

• add selenoprotein biotype (#197) (e4a43b6)

0.17.0 (2024-07-25)

Features

• add variant region condition for dups ending in 3' UTR (#192) (#195) (362909c)

0.16.3 (2024-07-16)

Bug Fixes

• BioType naming for Ig* types, derive Hash for BioType (#189) (62519c7)

0.16.2 (2024-07-14)

Bug Fixes

• add biotype vaultRNA_primary_transcript (#180) (d59783c)
• add biotype vaultRNA_primary_transcript (#183) (4345377)
• add partial field to cdot json representation struct (#179) (113a06a)
• add Serialize to data::cdot::json representations (#176) (2de1b8a)

0.16.1 (2024-06-10)

Bug Fixes

• use array instead of Vec for Codon representation (#169) (e455168)

Performance Improvements

• cache mappers, avoid allocations, codons are arrays (#172) (34acaf4)

0.16.0 (2024-03-05)

Features

• adding vertebrate mitochondrial code (#160) (#161) (eb6739b)

0.15.0 (2024-02-08)

Miscellaneous Chores

• bumping dependencies (#157) (6e75cd5)

0.14.1 (2023-11-19)

Bug Fixes

• allow import of BioType guide_RNA (#148) (0e1240f)

0.14.0 (2023-11-19)

Features

• adding support for selenoproteins (#145) (#146) (c5e21e2)

0.13.2 (2023-11-08)

Bug Fixes

• add more biotypes from cdot JSON for vep110 release (#141) (4cb7cb6)

0.13.1 (2023-11-08)

Bug Fixes

• adding back missing Gene::biotype member (#138) (84db645)

0.13.0 (2023-11-08)

Features

• make compatible with cdot v0.2.21 (#136) (c677b33)

0.12.0 (2023-10-21)

Features

• move out assemblies to biocommons_bioutils crate (#134) (#135) (d06bd28)

Bug Fixes

• problem with annotating stop_retained insertions (#131) (#132) (0f42d20)

0.11.0 (2023-09-18)

Features

• various dependency updates, bump version to 0.11.0 (#128) (09ed016)

0.10.1 (2023-07-04)

Bug Fixes

• properly configure dependabot for noodles (#119) (b539921)

0.10.0 (2023-07-04)

Miscellaneous Chores

• bump version to 0.10.0 (7bf4cbd)

0.9.0 (2023-06-12)

Features

• express existing thread safety (as most things are immutable) (#115) (0d6f241)

0.8.2 (2023-06-08)

Code Refactoring

• replace linked-hash-map by indexmap (#111) (#112) (f6d3ab4)

0.8.1 (2023-05-23)

Bug Fixes

• bump dependencies (#108) (af75b48)

0.8.0 (2023-05-23)

Features

• losen dependencies (#106) (c654507)

0.7.0 (2023-04-24)

Features

• proper error handling with enums and thiserror (#69) (#103) (add8248)

0.6.2 (2023-04-18)

Bug Fixes

• issue with non-dup insertion at start of protein (#99) (#100) (bc5b5cf)

0.6.1 (2023-04-06)

Bug Fixes

• cases where dup/inv goes beyond CDS (#89) (5d951b1)
• only warn on combining RefAlt with whole gene deletion (#92) (bff6c72)
• out of bound panic in case of long deletions (#91) (f0bcaa6)
• out of bounds issue for protein sequence creation (#93) (a40a5f5)
• out of bounds issue on 5'-to-3' shifting beyond CDS (#94) (4fccdb8)
• problem with variants in multi-stop codon txs (#95) (#96) (f25658c)

0.6.0 (2023-04-05)

Features

• make some tables visible in hgvs::sequences (#87) (d81bf8c)

0.5.2 (2023-04-04)

Performance Improvements

• further speeding up translate_cds code (#83) (#85) (60b071d)

0.5.1 (2023-04-03)

Performance Improvements

• tune translate_cds implementation (#80) (#81) (a608ba1)

0.5.0 (2023-03-31)

Features

• allow configuring that there is no genome sequence (#65) (cd5b7bb)
• replacing usages of unwrap() with expect or Result (#70) (#73) (94d6f88)

Bug Fixes

• case of missing stop codon (in particular ENSEMBL) (#72) (a44e28c)
• fixing wrong validation assumption about insertions (#64) (f58ff53)
• issue with transcripts missing stop codon (#67) (f70bb91)
• return error if problem in normalization (#71) (b656d2a)
• return error in normalization instead of unwrap() (#68) (8144db6)

0.4.0 (2023-03-27)

Features

• allow for disabling renormalization (#53) (b2f5dbe)
• improved normalizer configuration (#52) (2db5e92)
• make sequences module public (#54) (cfbb134)
• more comprehensive clone for field-less enums (#58) (3ada6b2)

Bug Fixes

• cases of empty sequence (#61) (0a6a109)
• fixing projection issues with cdot::json::Provider (#55) (edd0de9)
• fixing wrong validation assumption about insertions (#62) (bf027dc)
• interpret replace_reference condition (#49) (8326a55)
• issue with out of bounds deletion (#59) (475398d)
• remove ref length validation (#57) (763b7a3)
• truncate AA insertion at stop codon (#60) (54231b9)

0.3.1 (2023-03-13)

Bug Fixes

• deriving PartialEq and Eq for enums (#47) (abd946e)

0.3.0 (2023-03-13)

Features

• implement cdot data provider (#43) (#44) (3a8ed9d)

0.2.0 (2023-03-06)

Features

• implement PartialEq for Assembly (#40) (8808211)

Bug Fixes

• git lfs untrack 'src/static_data/**/.json' (#41) (fa1af68)

0.1.1 (2023-03-03)

Bug Fixes

• release 0.1.1 on crates.io (#38) (e318abf)

0.1.0 (2023-03-03)

Features

• implement AlignmentMapper (#14) (#15) (07b573d)
• implement Display for HgvsVariant and related types (#4) (#6) (8e81536)
• implement parsing of HGVS variants (#2) (#3) (dbcfd05)
• implement VariantMapper (#12) (#13) (44b10de)
• implementing AssemblyMapper (#7) (#35) (9f3e0f3)
• port over access to the UTA data structures (#10) (#11) (3e71e32)
• port over assembly info from bioutils (#8) (#9) (d583556)
• port over variant normalizer (#19) (#20) (8593068)
• porting over test_hgvs_variantmapper_gcp (#21) (#27) (7f925c8)
• porting over test_variantmapper_cp_real (#21) (#26) (6873324)
• start to port over test_hgvs_grammer_full.py (#21) (#31) (9d3e3b5)

Bug Fixes

• variant mapper g_to_t used wrong logic (#32) (040e2d3)

Changelog