Ecosyste.ms: Issues

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

#77 - docs: add Zenodo badge to README

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

#76 - chore: release 0.6.0

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

#75 - build: license in Cargo.toml rather than license-file

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

#74 - docs: adding badges to README

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

#73 - feat: add "serve pheno" REST API service (#72)

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

#72 - Implement REST service for Phenix-like prioritization of genes

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

#71 - chore: release 0.5.1

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

#70 - fix: region deserialization in sv query

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

#69 - fix: reciprocal overlap computation

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

#68 - feat: write out effective and matched genotype from rules (#64)

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

#67 - feat: implement gene allow lists for "sv query" (#65)

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

#66 - feat: annotate SVs with masked sequence overlap (#63)

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

#65 - Implement gene allow list filtration for SVs

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

#64 - Write out effective and matched genotype from rules

Issue - State: closed - Opened by holtgrewe about 2 years ago

#62 - fix: hgnc xlink path

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

#61 - chore: release 0.5.0

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

#60 - feat: serve genome browser tracks from database (#59)

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

#59 - Implement "file server" feature

Issue - State: closed - Opened by holtgrewe about 2 years ago

#58 - feat: add "server rest" sub command (#57)

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

#57 - Implement REST service to expose the public SV information

Issue - State: closed - Opened by holtgrewe about 2 years ago

#56 - chore: release 0.4.0

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

#55 - feat: implement "db compile" sub command (#54)

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

#54 - Implement "database compile" sub command

Issue - State: closed - Opened by holtgrewe about 2 years ago

#53 - feat: removing minimal overlap for pathogenic variants again

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

#52 - chore: release 0.3.0

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

#51 - feat: make TAD set configurable in query

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

#50 - feat: write out distance to next TAD boundary (#45)

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

#49 - feat: allow configuring whether missing call_info entry is pass (#47)

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

#48 - Refine known pathogenic region annotations

Issue - State: open - Opened by holtgrewe about 2 years ago

#46 - feat: write out bg db overlap counts in "sv query" (#44)

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

#45 - Write out distance to next TAD in "sv query"

Issue - State: closed - Opened by holtgrewe about 2 years ago

#44 - Write out background overlap counts in sv query

Issue - State: closed - Opened by holtgrewe about 2 years ago

#43 - feat: writing out payload.sv_length

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

#42 - chore: release 1.0.0

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago
Labels: autorelease: pending

#41 - fix!: enums serialization case and query issues

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

#40 - chore: release 0.3.0

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago
Labels: autorelease: pending

#39 - feat: make clinvar/pathogenic SV overlap configurable

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

#38 - chore: release 0.2.1

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

#37 - fix: pinning flatc-rust

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

#36 - ci: cache flatbuffers installation

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

#35 - feat: annotate ACMG and OMIM genes in "sv query" (#31)

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

#34 - chore: release 0.2.0

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

#33 - feat: adding --max-results for "sv query" sub command (#32)

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

#32 - Allow limiting the number of results

Issue - State: closed - Opened by holtgrewe about 2 years ago

#31 - Annotate ACMG and disease genes for svs

Issue - State: closed - Opened by holtgrewe about 2 years ago - 1 comment

#30 - ci: fix install-flatbuffers action with cargo

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

#29 - chore: release 0.1.0

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

#28 - feat: "sv query" now writes out TSV with information for a MVP

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

#27 - feat: annotating SVs with ClinVar VCV

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

#26 - Make "sv query" create reasonable output

Issue - State: closed - Opened by holtgrewe about 2 years ago

#25 - feat: make "sv query-next" feature-complete for a MVP (#24)

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

#24 - Make "sv query" feature complete for a MVP

Issue - State: closed - Opened by holtgrewe about 2 years ago

#23 - feat: read query from JSON file (#22)

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

#22 - Allow reading query from JSON file

Issue - State: closed - Opened by holtgrewe about 2 years ago

#21 - feat: using reasonble settings for sv query poc (#20)

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

#20 - Tune query parameters on some real-world data

Issue - State: closed - Opened by holtgrewe about 2 years ago

#19 - feat: add "sv build-bgdb" command (#18)

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

#18 - Implement "sv build-bgdb" sub command

Issue - State: closed - Opened by holtgrewe about 2 years ago

#17 - feat: switching CLI to multiple sub command levels

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

#16 - feat: PoC implementation of variant filtration (#15)

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

#15 - Implement filtration PoC

Issue - State: closed - Opened by holtgrewe about 2 years ago

#14 - feat: implement proper counting of background records (#13)

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

#13 - Implement proper counting of background records

Issue - State: closed - Opened by holtgrewe about 2 years ago - 1 comment

#12 - ci: codecov integration

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

#11 - feat: implement query schemas (10)

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

#10 - Implement query schemas

Issue - State: closed - Opened by holtgrewe about 2 years ago

#9 - perf: adjust interval types (#6)

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

#8 - Try rust-lapper for interval overlaps

Issue - State: closed - Opened by holtgrewe about 2 years ago - 1 comment

#7 - feat: implementing PoC query feature with SV VCF (#6)

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

#6 - Implement overlap query execution for SV VCF file

Issue - State: closed - Opened by holtgrewe about 2 years ago - 1 comment

#4 - Implement loading of background database

Issue - State: closed - Opened by holtgrewe about 2 years ago - 1 comment

#3 - chore: release 0.1.0

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

#2 - feat: bootstrapping sv-query sub command

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

#1 - docs: describe sv-query worker in README

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