bihealth/varfish-server-worker issues and pull requests

#278 - build(deps): bump aws-config from 0.56.1 to 1.1.1

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#277 - build(deps): bump the noodles group with 8 updates

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#276 - build(deps): bump clap-verbosity-flag from 2.1.0 to 2.1.1

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#275 - build(deps): bump aws-config from 0.56.1 to 1.0.3

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#274 - build(deps): bump the noodles group with 6 updates

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#273 - build(deps): bump async-compression from 0.4.4 to 0.4.5

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#272 - build(deps): bump derive-new from 0.5.9 to 0.6.0

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#271 - build(deps): bump the noodles group with 6 updates

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#270 - build(deps): bump aws-config from 0.56.1 to 1.0.1

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#269 - build(deps): bump serde from 1.0.190 to 1.0.193

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#268 - build(deps): bump enum-map from 2.7.0 to 2.7.3

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#267 - build(deps): bump aws-config from 0.56.1 to 0.101.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#266 - build(deps): bump the noodles group with 6 updates

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#265 - build(deps): bump prost from 0.12.1 to 0.12.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#264 - build(deps): bump prost-build from 0.12.1 to 0.12.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#263 - build(deps): bump tokio from 1.33.0 to 1.34.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#262 - build(deps): bump the noodles group with 6 updates

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#261 - build(deps): bump annonars from 0.24.4 to 0.24.5

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#260 - build(deps): bump aws-config from 0.56.1 to 0.57.1

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#259 - build(deps): bump clap from 4.4.6 to 4.4.8

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#258 - build(deps): bump hgvs from 0.12.0 to 0.13.2

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies

#257 - Support for ClinCNV TSV files

Issue - State: open - Opened by holtgrewe about 1 year ago
Labels: enhancement

#256 - Support and document FreeBayes

Issue - State: open - Opened by holtgrewe about 1 year ago
Labels: enhancement

#255 - build(deps): bump the noodles group with 4 updates

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#254 - build(deps): bump the noodles group with 3 updates

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#253 - build(deps): bump procfs from 0.15.1 to 0.16.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#252 - build(deps): bump the noodles group with 4 updates

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#251 - build(deps): bump indexmap from 2.0.2 to 2.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#250 - build(deps): bump aws-sdk-s3 from 0.34.0 to 0.35.0

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#249 - build(deps): bump serde_json from 1.0.107 to 1.0.108

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#248 - build(deps): bump tempfile from 3.8.0 to 3.8.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#247 - build(deps): bump aws-sdk-s3 from 0.33.0 to 0.34.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#246 - build(deps): bump serde from 1.0.189 to 1.0.190

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#245 - build(deps): bump futures from 0.3.28 to 0.3.29

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#244 - build(deps): bump the noodles group with 4 updates

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#243 - feat: add build of docker containers

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#242 - feat: implement I/O from/to S3 (#234)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#241 - feat: create .tbi for written .vcf.gz files (#233)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#240 - build(deps): bump the noodles group with 2 updates

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#239 - refactor: async I/O as prerequisite of using S3 (#234)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#238 - build(deps): bump thiserror from 1.0.49 to 1.0.50

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#237 - build(deps): bump clap-verbosity-flag from 2.0.1 to 2.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#236 - build(deps): bump enum-map from 2.6.3 to 2.7.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#235 - build(deps): bump the noodles group with 4 updates

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#234 - Implement I/O from/to S3

Issue - State: closed - Opened by holtgrewe over 1 year ago - 1 comment
Labels: enhancement

#233 - Create .tbi file for written .vcf.gz files

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#232 - Use in-house frequencies in "seqvars query"

Issue - State: open - Opened by holtgrewe over 1 year ago
Labels: enhancement

#231 - Properly handle X-recessive mode in seqvars query

Issue - State: open - Opened by holtgrewe over 1 year ago
Labels: enhancement

#230 - Differentiate between RocksDB error and no result

Issue - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#229 - Properly handle PAR regions in "seqvars aggreate"

Issue - State: closed - Opened by holtgrewe over 1 year ago - 1 comment
Labels: duplicate

#228 - build(deps): bump insta from 1.33.0 to 1.34.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#227 - build(deps): bump tracing from 0.1.37 to 0.1.39

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#226 - build(deps): bump strum_macros from 0.25.2 to 0.25.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#225 - build(deps): bump regex from 1.9.6 to 1.10.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#224 - build(deps): bump the noodles group with 4 updates

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#223 - feat: implement "seqvars query" command (#201)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#222 - feat: remove gene regions from "strucvars query" database enhancement (#221)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#221 - Remove gene regions from "strucvars query" database

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#220 - feat: adjust "strucvars query" to read ingested VCFs (#202)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#219 - feat: transform "db to-bin" to "strucvars txt-to-bin" (#218)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#218 - Transform "db to-bin" to "strucvars txt-to-bin"

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#217 - feat: transform "db mk-inhouse" to "strucvars aggregate" (#212)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#216 - Properly handle PAR regions in aggregate

Issue - State: open - Opened by holtgrewe over 1 year ago
Labels: enhancement

#215 - feat: write out fileDate on ingest (#210)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#214 - feat: adding "seqvars aggregate" command (#211)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#213 - feat: implementing "seqvars prefilter" (#209)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#212 - Transform strucvars "db mk-inhouse" to "strucvars aggregate"

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#211 - Implement "seqvars aggregate"

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#210 - Write out more information in seqvars/strucvars ingest headers

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#209 - Implement "seqvars prefilter" command

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#208 - feat: implement "strucvars ingest" command (#200)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#207 - chore: release 0.11.0

Pull Request - State: open - Opened by varfish-bot over 1 year ago - 1 comment
Labels: autorelease: pending

#206 - feat: implement "seqvars ingest" command (#199)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#205 - chore: remove direct dependency to lazy_static (#98)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#204 - feat: implement parsing of clinvar-data-jsonl data (#198)

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#203 - docs: updating README.md

Pull Request - State: closed - Opened by holtgrewe over 1 year ago

#202 - Implement "strucvars query" command

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#201 - Implement "seqvars query" command

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#200 - Implement "strucvars ingest" command

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#199 - Implement "seqvars ingest" command

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#198 - Implement parsing of clinvar-data-jsonl variants

Issue - State: closed - Opened by holtgrewe over 1 year ago
Labels: enhancement

#197 - chore: bumping dependencies

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#196 - chore: release 0.10.2

Pull Request - State: closed - Opened by varfish-bot over 1 year ago - 2 comments
Labels: autorelease: tagged

#195 - build(deps): bump the noodles group with 1 update

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#194 - build(deps): bump annonars dependency

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment
Labels: dependencies

#193 - fix: resolve prost from_i32 deprecation

Pull Request - State: closed - Opened by holtgrewe over 1 year ago - 1 comment

#192 - build(deps): bump serde_json from 1.0.106 to 1.0.107

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#191 - build(deps): bump insta from 1.31.0 to 1.32.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#190 - build(deps): bump prost from 0.12.0 to 0.12.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#189 - build(deps): bump chrono from 0.4.30 to 0.4.31

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#188 - build(deps): bump clap from 4.4.2 to 4.4.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#187 - build(deps): bump bio from 1.3.1 to 1.4.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#186 - build(deps): bump the noodles group with 2 updates

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#185 - build(deps): bump chrono from 0.4.26 to 0.4.30

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#184 - build(deps): bump prost-build from 0.11.9 to 0.12.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#183 - build(deps): bump regex from 1.9.3 to 1.9.5

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#182 - build(deps): bump enum-map from 2.6.1 to 2.6.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#181 - build(deps): bump serde_json from 1.0.105 to 1.0.106

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#180 - build(deps): bump prost from 0.11.9 to 0.12.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#179 - build(deps): bump thiserror from 1.0.47 to 1.0.48

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

GitHub / bihealth/varfish-server-worker issues and pull requests