Changelog

0.17.0 (2024-10-30)

Features

inhouse freqs useable in seqvars query (#232) (#522) (45bec0c)

0.16.1 (2024-10-30)

Bug Fixes

seqvars aggregate async runtime error (#519) (#520) (3911afe)

0.16.0 (2024-10-28)

⚠ BREAKING CHANGES

adjusting max_af to max_carriers for inhouse (#512)
more protobuf cleaning (#511)

Code Refactoring

adjusting max_af to max_carriers for inhouse (#512) (c212b44)
consolidating protobuf definitions (#508) (#509) (0edcf98)
more protobuf cleaning (#511) (06ebb8a)

0.15.0 (2024-10-24)

Features

adding more annotations to output (#504) (#505) (0225f81)

Bug Fixes

typos in score field names (#507) (85da7e6)

0.14.0 (2024-10-09)

Features

add mode of inheritance from HPO (#493) (2da2b86)

Bug Fixes

bump mehari to escape clinvar output string (#485) (#488) (e0e2370)
suppress unknown consequence errors (#491) (c95ed79)
suppress unknown consequence errors (#492) (bfe718d)

0.13.2 (2024-10-07)

Bug Fixes

anc can be float or int (#478) (0c37d30)

0.13.1 (2024-10-07)

Bug Fixes

add missing consequence conversion (#454) (843922a)
changing protobuf and others as needed (#455) (2718a6e)
make reading from S3 work and bump mehari (#452) (13a106a)
proper handling of FORMAT/amq (#477) (e1f89a0)

0.13.0 (2024-08-06)

⚠ BREAKING CHANGES

write out hom. ref. count in seqvars aggregate (#428) (#429)
cleanup protobufs to best practices (#423) (#425)
refactory query schema to use protobuf (#374) (#419)

Features

cleanup protobufs to best practices (#423) (#425) (48a3144)
introduce protobuf schema for seqvars query output (#375) (#430) (214c8e9)
message members explicitely optional for protobufs (#431) (1458aad)
refactory query schema to use protobuf (#374) (#419) (0e14e16)
write out hom. ref. count in seqvars aggregate (#428) (#429) (3830a55)

Bug Fixes

allow parsing FORMAT/anc as Float/f32 (#414) (bf4634b)

0.12.0 (2024-06-19)

Features

implement file identifier mappings (#364) (#365) (57db49a)

Bug Fixes

noodles and other deps (#378) (#379) (4dc0f94)
using custom S3 endpoint (#362) (06334e6)

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)

0.10.2 (2023-10-04)

Bug Fixes

resolve prost from_i32 deprecation (#193) (fc4cd3e)

0.10.1 (2023-07-31)

Bug Fixes

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

0.10.0 (2023-07-25)

Features

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

0.9.0 (2023-07-05)

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)

0.8.0 (2023-06-28)

⚠ 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)

0.7.0 (2023-06-09)

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)

0.6.1 (2023-05-03)

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)

0.6.0 (2023-05-02)

Features

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

0.5.1 (2023-03-14)

Bug Fixes

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

0.5.0 (2023-02-13)

Features

annotate SVs with masked sequence overlap (#63) (#66) (0fd9403)
implement gene allow lists for "sv query" (#65) (#67) (aa9da21)
serve genome browser tracks from database (#59) (#60) (040c522)
write out effective and matched genotype from rules (#64) (#68) (2c2c793)

Bug Fixes

hgnc xlink path (#62) (985cc33)

0.4.0 (2023-02-09)

Features

add "server rest" sub command (#57) (#58) (4b41010)
implement "db compile" sub command (#54) (#55) (7aa8c69)

0.3.0 (2023-02-01)

⚠ BREAKING CHANGES

enums serialization case and query issues (#41)

Features

allow configuring whether missing call_info entry is pass (#47) (#49) (4d0f64d)
make clinvar/pathogenic SV overlap configurable (#39) (af36bd4)
make TAD set configurable in query (#51) (82d4995)
removing minimal overlap for pathogenic variants again (#53) (3a5d427)
write out bg db overlap counts in "sv query" (#44) (#46) (7286d0d)
write out distance to next TAD boundary (#45) (#50) (5ef72f3)
writing out payload.sv_length (#43) (368621d)

Bug Fixes

enums serialization case and query issues (#41) (7cd73aa)

Miscellaneous Chores

set next 0.3.0 (101615d)

0.2.1 (2023-01-31)

Bug Fixes

pinning flatc-rust (#37) (e9d1d89)

0.2.0 (2023-01-31)

Features

adding --max-results for "sv query" sub command (#32) (#33) (4aa7094)
annotate ACMG and OMIM genes in "sv query" (#31) (#35) (9058e2a)

0.1.0 (2023-01-30)

Features

"sv query" now writes out TSV with information for a MVP (#28) (6a928c8)
add "sv build-bgdb" command (#18) (#19) (00cdf41)
annotating SVs with ClinVar VCV (#27) (14af2bc)
bootstrapping sv-query sub command (#2) (9cb0c95)
implement proper counting of background records (#13) (#14) (a0965cc)
implement public/in-house SV database interval tree construction (#4) (#5) (03442aa)
implement query schemas (10) (#11) (cc087d7)
implementing PoC query feature with SV VCF (#6) (#7) (925ebd8)
make "sv query-next" feature-complete for a MVP (#24) (#25) (b7c873c)
PoC implementation of variant filtration (#15) (#16) (12201ca)
read query from JSON file (#22) (#23) (4e41fbc)
switching CLI to multiple sub command levels (#17) (9af47df)
using reasonble settings for sv query poc (#20) (#21) (26c0ba0)

Performance Improvements

adjust interval types (#6) (#9) (76d254b)