v0.11.0

0.11.0 (2024-02-27)

Features

• add build of docker containers (#243) (c455e25)
• adding "seqvars aggregate" command (#211) (#214) (d6db0b7)
• adjust "strucvars query" to read ingested VCFs (#202) (#220) (1fb3c58)
• allow importing gnomAD SV/CNV v4 as background db (#295) (#310) (ce9b391)
• create .tbi for written .vcf.gz files (#233) (#241) (be99642)
• implement "seqvars ingest" command (#199) (#206) (21b965c)
• implement "seqvars query" command (#201) (#223) (a7cb0bd)
• implement "strucvars ingest" command (#200) (#208) (a783ef3)
• implement I/O from/to S3 (#234) (#242) (414bb5d)
• implement ingest and aggregate for sniffles2 (#296) (#312) (6432365)
• implement ingest for Clair3+GLNexus (#297) (#311) (4144003)
• implement parsing of clinvar-data-jsonl data (#198) (#204) (e0ea7ac)
• implementing "seqvars prefilter" (#209) (#213) (984dc8b)
• remove gene regions from "strucvars query" database enhancement (#221) (#222) (28663b6)
• transform "db mk-inhouse" to "strucvars aggregate" (#212) (#217) (b51f027)
• transform "db to-bin" to "strucvars txt-to-bin" (#218) (#219) (ea6e387)
• unify database names in strucvar filtration (#307) (#308) (43413d4)
• write out fileDate on ingest (#210) (#215) (7731958)

Bug Fixes

• normalize patho-mms.bed => patho_mms.bed (#315) (48afb7d)

varfish-server-worker v0.10.2

Bug Fixes

• resolve prost from_i32 deprecation (#193) (fc4cd3e)

varfish-server-worker v0.10.1

Bug Fixes

• allow HGNC IDs in gene allow list (#153) (416bf28)

varfish-server-worker v0.10.0

Features

• write out HGNC ids for sv query results (#150) (#151) (9e1074b)

varfish-server-worker v0.9.0

Features

• adding allelic balance for SVs (#127) (564a7ec)
• allow filtering SVs based on effect on transcript (#129) (#134) (1aab8c8)

Bug Fixes

• dependabot config and updates (#133) (006e306)
• removing unused dependencies (#124) (2cee74b)
• specification of genomic range in query (#126) (6eddaef)

varfish-server-worker v0.8.0

⚠ BREAKING CHANGES

• remove REST server related code (#122) (#123)
• replace db-compile with per-output commands (#112) (#121)

Code Refactoring

• remove code that was moved to viguno/annonars (#116) (#117) (50099dd)
• remove REST server related code (#122) (#123) (0b68809)
• replace db-compile with per-output commands (#112) (#121) (5da2799)

varfish-server-worker v0.7.0

Features

• add "db genes query" command (#109) (27e995c)
• adding "pheno prune" command against all-parents annotation (#100) (#114) (c77b2d4)
• adding genes database (#85) (#90) (634e281)
• adding sequence variant databases (#94) (74f985a)
• individual paths for "db genes build" (#106) (0a10a4e)
• move from flatbuffers to protocol buffers (#89) (#99) (cff7ace)
• support for dbNSFP gene information (#97) (#102) (0448bcb)
• use protobuf/prost for gene information storage (#96) (#101) (6a97fb6)

varfish-server-worker v0.6.1

Bug Fixes

• "db mk-inhouse" command for breakends (#79) (9b33e1d)
• command "sv query" for types BND and INS (#81) (5be2274)
• correctly interpret "callers" column (#82) (8e083c8)
• overlap queries for BND and INS (#83) (4de4eda)

varfish-server-worker v0.6.0

Features

• add "serve pheno" REST API service (#72) (#73) (17c9dd5)

varfish-server-worker v0.5.1

Bug Fixes

• reciprocal overlap computation (#69) (6165d9f)
• region deserialization in sv query (#70) (7a577e3)