CHANGELOG.md

Changelog

0.29.6 (2024-10-16)

Bug Fixes

• add missing librocksdb8.9 to Dockerfile (#584) (f9bd018)
• skip REF-only records (#576) (688b968)

0.29.5 (2024-10-08)

Continuous Integration

• adding dependency libsqlite3-dev (#574) (08bdc10)

0.29.4 (2024-10-08)

Continuous Integration

• bump ubuntu to 24.04 (#572) (0ef8f7d)

0.29.3 (2024-10-08)

Bug Fixes

• install libsnappy-dev in CI (#570) (1169479)

0.29.2 (2024-10-08)

Continuous Integration

• install rocksdb dependencies in CI (#568) (c1dfe6f)

0.29.1 (2024-10-08)

Bug Fixes

• percent encoding clinvar annotation (#553) (#566) (6540520)

0.29.0 (2024-10-07)

Features

• Add catch all tag "Other" (#558) (c709a36)

0.28.1 (2024-09-02)

Bug Fixes

• disregard tsv output order in brca2_zar1l test (#529) (d5e1066)
• make seqvar annotators public for varfish-server-worker (#528) (22610d1)

0.28.0 (2024-08-19)

Features

• add "db merge" subcommand (#517) (3c7b514)

0.27.0 (2024-08-16)

Features

• refactor annotate seqvars cli (#510) (915b30a)

Bug Fixes

• codon deletion right in front of stop codon is not a stop_gained (#515) (48fd896)

0.26.1 (2024-08-07)

Bug Fixes

• Add gencode primary tag (#509) (a6c8566)
• for fake-rna-* transcripts for refseq MT, add fake version as well (#507) (f296e5d)

0.26.0 (2024-08-02)

⚠ BREAKING CHANGES

• refactor DB create (#456)

Features

• Make path-input-ped optional (#472) (e6cf526)
• refactor DB create (#456) (c0fd47a)

0.25.7 (2024-06-18)

Bug Fixes

• make cargo release work again (#469) (a3f85fd)

0.25.6 (2024-06-18)

Bug Fixes

• bump annonars dependency (#462) (83b47d3)
• copy over keys::Var::from_vcf_allele from annonars to avoid noodles version conflicts in the future (#461) (952d8a9)
• make previously public code public again (#465) (0ef7652)
• Performance improvements (#444) (b996795)

0.25.5 (2024-03-29)

Bug Fixes

• actually produce one tsv record per gene+annotations (#413) (1ccabbb)

0.25.4 (2024-03-08)

Bug Fixes

• stop codon issue for Ensembl chrMT transcripts (#401) (895e6f6)

0.25.3 (2024-03-07)

Bug Fixes

• variants on chrX and chrY were erroneously ignored (#399) (0acc542)

0.25.2 (2024-03-06)

Bug Fixes

• strucvars/csq should not double-HGNC prefix gene IDs (#397) (b09782c)

0.25.1 (2024-03-06)

Bug Fixes

• move assertion on chrMT transcripts (#395) (6a03acf)

0.25.0 (2024-03-05)

Features

• enable using ENSEMBL chrMT transcript (#381) (#393) (91b4610)

0.24.2 (2024-03-04)

Features

• report MANE transcript counts in "db create" (#378) (2826b1a)

Bug Fixes

• make server genes/tx return empty page on missing gene (#385) (#387) (f5d4a2f)
• miniscule fix to example URL output (#382) (dfb8824)
• warn on missing transcripts rather than failing (#380) (#384) (eaa99ae)

Miscellaneous Chores

• release as v0.24.2 (576dbb6)

0.24.1 (2024-02-26)

Miscellaneous Chores

• cleanup test db bootstrapping (#370) (#371) (9479cd0)

0.24.0 (2024-02-26)

Features

• adding "mehari db subset" command (#367) (#368) (14044e3)

0.23.2 (2024-02-22)

Bug Fixes

• handling missing FORMAT/AD values (".") (#365) (170ee00)

0.23.1 (2024-02-22)

Bug Fixes

• work around issue with glnexus #362 (#363) (77afb96)

0.23.0 (2024-02-21)

Features

• adding support for Sniffles2 (#357) (#358) (01641d7)
• script fix_glnexus.py prepare GLNexus output for noodles (#356) (#361) (98d8233)

0.22.0 (2024-02-09)

Features

• adding /genes/txs endpoint for server (#339) (#340) (59dbaaf)

0.21.2 (2024-02-01)

Miscellaneous Chores

• applying org change (bihealth => varfish-org) (#325) (8db8db0)

0.21.1 (2023-12-01)

Bug Fixes

• bumping annonars dependency to fix protobuf issues (#287) (007dd12)

0.21.0 (2023-11-22)

⚠ BREAKING CHANGES

• adjusting enum values (#279)

Bug Fixes

• adjusting enum values (#279) (6921b39)

0.20.0 (2023-11-21)

⚠ BREAKING CHANGES

• moving crate::pbs::mehari => crate::pbs (#277)

Code Refactoring

• moving crate::pbs::mehari => crate::pbs (#277) (e44211e)

0.19.1 (2023-11-21)

Bug Fixes

• copy in protobufs into docker builds (#275) (f4d4c20)

0.19.0 (2023-11-21)

⚠ BREAKING CHANGES

• serializing protobufs pbjson-build (#272) (#273)

Features

• serializing protobufs pbjson-build (#272) (#273) (0f948f7)

0.18.1 (2023-11-19)

Miscellaneous Chores

• update dependencies (#268) (a3c379e)

0.18.0 (2023-11-19)

Features

• properly handle selenoprotein import from cdot (#224) (#265) (20137ad)

0.17.1 (2023-11-15)

Bug Fixes

• fixing implementation of Provider::get_tx_for_gene (#262) (42945dd)

0.17.0 (2023-11-10)

⚠ BREAKING CHANGES

• make --path-input-ped for seqvars annotation required (#194) (#255)

Features

• adding helper script to fix FreeBayes VCF (#252) (#254) (4bd5461)
• adding support for ClinCNV (#253) (#257) (aba47c9)

Bug Fixes

• make --path-input-ped for seqvars annotation required (#194) (#255) (de832b2)

0.16.0 (2023-11-09)

Features

• allow user to select transcript source on CLI (#247) (#249) (caab82e)
• update tx support to latest cdot with MANE label transfer (#245) (#248) (b69e80d)

0.15.2 (2023-10-28)

Bug Fixes

• remove second async runtime creation (#234) (a6c3e06)

0.15.1 (2023-10-24)

Bug Fixes

• properly flush and sync all writers (#232) (2772565)

0.15.0 (2023-10-23)

Features

• adding async I/O, espec. for SV caller guessing (#230) (33c0e8e)

0.14.3 (2023-10-22)

Bug Fixes

• index out of bounds error in stop_retained variant (#226) (#228) (cc8d440)

0.14.2 (2023-10-21)

Bug Fixes

• make distance to next exon correct (#222) (#223) (cad307f)
• switching from unmaintained tempdir to tempfile (#227) (a7b0e08)

0.14.1 (2023-10-19)

Bug Fixes

• dependency bumps, including annonars (#220) (ac57c66)

0.14.0 (2023-10-18)

Features

• bump annonars, write out VCV+RCV+clinsig (#217) (0d7b6d8)

0.13.0 (2023-10-16)

Features

• derive Clone and strum::EnumIter on more enums (#213) (cc61a66)
• implementing Default for AnnField (#215) (73b1be4)
• proper serde renames for Consequence and PutativeImpact (#214) (02286fa)

Bug Fixes

• documenting "AN" as alleles rather than samples (#206) (62ee63b)

0.12.0 (2023-10-09)

Features

• expose strucvars annotation for worker aggregation command (#204) (0f730ce)

0.11.0 (2023-10-06)

Features

• allow BGZ files for guess_sv_caller (#203) (31dc430)

Bug Fixes

• use new Debug trait implementation in Sample (#201) (7fafcbf)

0.10.0 (2023-10-05)

Features

• expose clinvar annotation (#199) (3bcbf32)

Bug Fixes

• Make mitochondrial DRAGEN calls not fail mehari (#195) (e170120)

0.9.0 (2023-10-05)

Features

• exposing more functions for sequence variant annotation (#198) (06a8dee)
• exposing utility functions for pedigree / vcf building (#196) (7d77f35)

0.8.0 (2023-10-02)

Features

• adding REST endpoint for SV annotation (#188) (9e14c09)
• snake_case in REST APIs and rename /tx/csq to /seqvars/csq (#150) (#189) (e1021ed)

0.7.0 (2023-09-18)

Features

• bump dependencies (especially noodles) (#179) (34b540c)
• support for MELT VCF files (#181) (831e9af)

Bug Fixes

• Allow '.' genotypes (#178) (6d0c5b8)

0.6.2 (2023-07-17)

Bug Fixes

• adjust clinvar column family name (#138) (95b7ffb)

0.6.1 (2023-07-11)

Bug Fixes

• strucvars annotate TSV output header (#80) (#130) (f4d3315)

0.6.0 (2023-07-04)

Features

• mehari becomes available as a library (#118) (59bb41a)

Bug Fixes

• fix Dockerfile by removing two-stage process (#128) (0346977)
• wrong default of PATH_DB in Dockerfile (#111) (51e10cc)

0.5.7 (2023-06-20)

Bug Fixes

• adding libsqlite3-0 to the Docker image (#109) (be832fb)

0.5.6 (2023-06-19)

Bug Fixes

• dependency bump to make code compile again (#104) (8199d3e)
• docker build version in CI (#107) (9a0799f)

Build System

• some small fixes to CI (#106) (fb54df0)

0.5.5 (2023-06-19)

Build System

• fix Docker builds (#102) (6366e65)

0.5.4 (2023-06-17)

Build System

• adjust Docker builds for PRs and branches (#100) (e38388b)

0.5.3 (2023-06-16)

Miscellaneous Chores

• re-release as v0.5.3 (12aed0a)

0.5.2 (2023-06-14)

Bug Fixes

• docker build in CI (#96) (ba34c03)

0.5.1 (2023-06-13)

Features

• build Docker image in CI (#92) (c72d804)

Bug Fixes

• add Cargo.lock to git (#94) (f7c4f03)
• remove unused dependencies (#95) (a1e1054)

0.5.0 (2023-06-12)

Features

• REST server for variant consequence prediction (#18) (#90) (b8c5a7b)

0.4.1 (2023-06-12)

Bug Fixes

• properly flush stream in "db create txs" (#88) (95458f3)

0.4.0 (2023-06-08)

Features

• move clinvar database code (import etc.) to annonars (#86) (457be46)
• switch to annonars for frequency db creation (#81,#77,#20) (#83) (bb27686)

Code Refactoring

• move from linked-hash-map to indexmap (#82) (#87) (f9e354d)

0.3.1 (2023-05-04)

Bug Fixes

• use copy number to fill in genotypes for CNVs (#72) (5585a08)

0.3.0 (2023-05-03)

Features

• add genotype counting (#70) (c40f83c)

Bug Fixes

• only copy samples from input VCF header (#69) (316b123)

0.2.1 (2023-05-02)

Bug Fixes

• adjust non-adjacent exon recognition (#67) (96437e4)
• allow multiple bases in BND ALT (#63) (e5b93d5)
• properly recognize .gz/.zst extension (#66) (6960521)
• skipping "*" ALT alleles (#65) (95b2b61)

0.2.0 (2023-04-24)

Features

• allow annotation from maelstorm cov/mq BED files (#51) (#55) (f3966ac)
• annotation of structural variants (#46) (#52) (8da1d38)
• change database path setup (#48) (#60) (b26671f)
• implement command to copy rocksdb database (#45) (#47) (3c8543f)
• switch from flatbuffers to protobuf (#15) (#57) (3fe3322)

Bug Fixes

• issue on negative CDS position (#49) (#58) (9a63e30)

0.1.1 (2023-04-06)

Bug Fixes

• release 0.1.1 (5565d93)

0.1.0 (2023-04-06)

Features

• adding command "db create seqvars-clinvar" (#24) (#25) (fd4c523)
• allow mehari to write out VarFish compatible TSV (#34) (#35) (72c6832)
• command "verify seqvars" allows to compare to VEP (#21) (#37) (b8761e3)
• frequency annotation with database (#12) (#13) (f63f8c2)
• implement seqvar frequency db construction (#2) (#5) (01fc64c)
• implementing "annotate seqvars" (#3) (#7) (6400ed1)
• transcript based annotation (#11) (#14) (6677899)
• transcript database building (#1) (#8) (bcff954)

Bug Fixes

• allow loading JSON from .gz files (#22) (cefd950)
• issues occuring when annotating real data (#28) (0636d49)

Changelog