bihealth/varfish-server-worker issues and pull requests

#178 - build(deps): bump clap from 4.4.0 to 4.4.2

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

#177 - build(deps): bump flate2 from 1.0.26 to 1.0.27

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

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

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

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

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

#174 - build(deps): bump clap from 4.3.21 to 4.4.0

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

#173 - build(deps): bump serde_with from 3.2.0 to 3.3.0

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

#172 - build(deps): bump anyhow from 1.0.72 to 1.0.75

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

#171 - build(deps): bump clap from 4.3.21 to 4.3.23

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#170 - build(deps): bump thiserror from 1.0.44 to 1.0.47

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

#169 - build(deps): bump serde_json from 1.0.104 to 1.0.105

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

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

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#167 - build(deps): bump rstest from 0.18.1 to 0.18.2

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

#166 - build(deps): bump log from 0.4.19 to 0.4.20

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

#165 - build(deps): bump clap from 4.3.19 to 4.3.21

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

#164 - build(deps): bump regex from 1.9.1 to 1.9.3

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

#163 - build(deps): bump strum_macros from 0.25.1 to 0.25.2

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

#162 - build(deps): bump serde_json from 1.0.103 to 1.0.104

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

#161 - build(deps): bump enum-map from 2.6.0 to 2.6.1

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

#160 - build(deps): bump serde_with from 3.0.0 to 3.2.0

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

#159 - build(deps): bump uuid from 1.4.0 to 1.4.1

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

#158 - build(deps): bump thiserror from 1.0.41 to 1.0.44

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

#157 - build(deps): bump serde_with from 3.0.0 to 3.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#156 - build(deps): bump serde_test from 1.0.175 to 1.0.176

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

#155 - build(deps): bump anyhow from 1.0.71 to 1.0.72

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

#154 - chore: release 0.10.1

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

#153 - fix: allow HGNC IDs in gene allow list

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

#152 - chore: release 0.10.0

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

#151 - feat: write out HGNC ids for sv query results (#150)

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

#150 - Write out HGNC IDs for in sv query results.

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

#149 - build(deps): bump serde_test from 1.0.166 to 1.0.175

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

#148 - build(deps): bump serde_json from 1.0.100 to 1.0.103

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

#147 - build(deps): bump clap from 4.3.11 to 4.3.19

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

#146 - build(deps): bump insta from 1.30.0 to 1.31.0

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

#145 - build(deps): bump pretty_assertions from 1.3.0 to 1.4.0

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

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

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

#143 - build(deps): bump serde_test from 1.0.166 to 1.0.171

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#142 - build(deps): bump regex from 1.9.0 to 1.9.1

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

#141 - build(deps): bump serde from 1.0.166 to 1.0.168

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

#140 - build(deps): bump clap from 4.3.10 to 4.3.11

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

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

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

#138 - build(deps): bump regex from 1.8.4 to 1.9.0

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

#137 - build(deps): bump rstest from 0.17.0 to 0.18.1

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

#136 - build(deps): bump serde_json from 1.0.99 to 1.0.100

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

#135 - build(deps): bump thiserror from 1.0.40 to 1.0.41

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

#134 - feat: allow filtering SVs based on effect on transcript (#129)

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

#133 - fix: dependabot config and updates

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

#132 - docs: fix terraform instructions in README

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

#131 - chore: improve test coverage

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

#130 - ci: use bot token (for varfish-bot) in release-please

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

#129 - Allow filtering SVs based on effect on transcripts

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

#128 - chore: release 0.9.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 2 comments
Labels: autorelease: tagged

#127 - feat: adding allelic balance for SVs

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

#126 - fix: specification of genomic range in query

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

#125 - chore: release 0.8.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: autorelease: pending

#124 - fix: removing unused dependencies

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

#123 - refactor!: remove REST server related code (#122)

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

#122 - Remove REST server-related code

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

#121 - refactor!: replace db-compile with per-output commands (#112)

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

#120 - build: remove unused dependencies

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

#119 - chore: release 0.8.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#118 - chore: add PR template, automerge action, terraform

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

#117 - refactor: remove code that was moved to viguno/annonars (#116)

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

#116 - Remove code moved to viguno/annonars

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

#115 - refactor: move db::pbs into its own file, remove "db copy"

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

#114 - feat: adding "pheno prune" command against all-parents annotation (#100)

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

#113 - Use gene regions from mehari transcripts

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

#112 - Replace "db compile" command by per-output commands.

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

#111 - Add mim2gene information to genes

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

#110 - Harmonize the cli command names

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

#109 - feat: add "db genes query" command

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

#108 - chore: remove clis forwarded to annonars

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

#107 - chore: remove clinvar.proto (now in annonars)

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

#106 - feat: individual paths for "db genes build"

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

#105 - chore(deps): updating all dependencies

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

#104 - chore: bump dependencies (incl. annonars)

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

#102 - feat: support for dbNSFP gene information (#97)

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

#101 - feat: use protobuf/prost for gene information storage (#96)

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

#100 - Perform tuning of phenix-like prioritization

Issue - State: closed - Opened by holtgrewe over 1 year ago - 2 comments
Labels: enhancement

#99 - feat: move from flatbuffers to protocol buffers (#89)

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

#98 - Replace lazy_static with once_cell

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

#97 - Add support for importing dbNSFP gene information

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

#96 - Use prost for storing gene information

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

#95 - Add "spec" JSON files

Issue - State: open - Opened by holtgrewe almost 2 years ago - 1 comment
Labels: enhancement

#94 - feat: adding sequence variant databases

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#93 - Implement REST service to serve per-variant information

Issue - State: closed - Opened by holtgrewe almost 2 years ago
Labels: enhancement

#92 - Bring back KEGG per-gene information.

Issue - State: open - Opened by holtgrewe almost 2 years ago
Labels: enhancement

#91 - chore: release 0.7.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 2 comments
Labels: autorelease: tagged

#90 - feat: adding genes database (#85)

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#89 - Replace flatbuffers usage by protobuffers

Issue - State: closed - Opened by holtgrewe almost 2 years ago
Labels: enhancement

#88 - Implement REST server to serve clinvar information

Issue - State: open - Opened by holtgrewe almost 2 years ago
Labels: enhancement

#87 - Store GTEx information per gene

Issue - State: open - Opened by holtgrewe almost 2 years ago
Labels: enhancement

#86 - Pull more information from NCBI Entrez

Issue - State: open - Opened by holtgrewe almost 2 years ago
Labels: enhancement

#85 - Implement REST service to serve static gene information

Issue - State: closed - Opened by holtgrewe almost 2 years ago - 2 comments
Labels: enhancement

#84 - chore: add issue templates

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

#83 - fix: overlap queries for BND and INS

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#82 - fix: correctly interpret "callers" column

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#81 - fix: command "sv query" for types BND and INS

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#80 - chore: release 0.6.1

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#79 - fix: "db mk-inhouse" command for breakends

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago - 1 comment

#78 - ci: use GitHub token for protoc setup

Pull Request - State: closed - Opened by holtgrewe almost 2 years ago

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