Clinical-Genomics/loqusdb issues and pull requests

#144 - Update the description of the Frq INFO tag

Pull Request - State: closed - Opened by ramprasadn 23 days ago - 1 comment

#143 - Add linters

Pull Request - State: closed - Opened by henrikstranneheim 4 months ago - 2 comments

#142 - feat(codeowners): Add

Pull Request - State: closed - Opened by henrikstranneheim 4 months ago - 1 comment

#141 - fix(action): Bump

Pull Request - State: closed - Opened by henrikstranneheim 4 months ago

#140 - fix(action): Bump

Pull Request - State: closed - Opened by henrikstranneheim 4 months ago

#139 - fix(action): Bump

Pull Request - State: closed - Opened by henrikstranneheim 4 months ago

#138 - 77Fix version

Pull Request - State: closed - Opened by henrikstranneheim 4 months ago

#137 - fix(action): Bump

Pull Request - State: closed - Opened by henrikstranneheim 4 months ago

#136 - migrate test coverage to codecov

Issue - State: open - Opened by dnil 4 months ago

#135 - WIP

Pull Request - State: closed - Opened by henrikstranneheim 4 months ago - 17 comments

#134 - Address security issue in setuptools < 70.0

Issue - State: closed - Opened by northwestwitch 7 months ago

#133 - Update setuptools to address a security issue

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 1 comment

#132 - Update issue templates

Pull Request - State: closed - Opened by dnil 8 months ago

#131 - Fix #117 corollary - if QUAL is . set to 0

Pull Request - State: closed - Opened by dnil 11 months ago - 2 comments

#130 - No frequencies shown for mitochondrial variants

Issue - State: open - Opened by Jakob37 about 1 year ago
Labels: question

#129 - Fix #127 - optimise index for sv queries

Pull Request - State: closed - Opened by dnil about 1 year ago - 7 comments

#128 - Handle TIDDIT style SV type names

Pull Request - State: open - Opened by dnil about 1 year ago

#127 - Improve indexes

Issue - State: closed - Opened by northwestwitch about 1 year ago
Labels: enhancement

#126 - index missing on loqusdb-tumor

Issue - State: closed - Opened by dnil about 1 year ago - 2 comments

#125 - Bump pip from 23.1.2 to 23.3

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

#124 - Unfreeze PyMongo and replace deprecated count() with count_documents()

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 3 comments

#123 - Fix installing error due to PyYaml version

Pull Request - State: closed - Opened by northwestwitch over 1 year ago - 6 comments

#122 - Deprecated config in `setup.cfg`

Issue - State: closed - Opened by northwestwitch over 1 year ago - 1 comment
Labels: bug

#121 - unfreeze PyMongo

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

#120 - Mei variant

Pull Request - State: open - Opened by dnil over 1 year ago

#119 - Store MEI variants

Issue - State: open - Opened by dnil over 1 year ago

#118 - Fix #117 - add a flag to allow QUAL filter instead of GQ

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

#117 - Use QUAL for filtering in addition to GQ

Issue - State: closed - Opened by dnil over 1 year ago - 6 comments

#116 - Check bad variant search - susceptible to missing reverse variant query?

Issue - State: open - Opened by dnil almost 2 years ago

#115 - log homozygous families

Issue - State: open - Opened by dnil almost 2 years ago - 4 comments

#114 - fix(treshold -> threshold)

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

#113 - Bump setuptools from 59.2.0 to 65.5.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#112 - Loqusdb upload SV variant type

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

#111 - Option to select individual for upload

Pull Request - State: open - Opened by dnil about 2 years ago - 2 comments

#110 - Add an option to loqusdb to select which sample to upload / check identity in a multi sample vcf without bed

Issue - State: open - Opened by dnil about 2 years ago - 1 comment

#109 - Case count for non-existing variant throws TypeError

Issue - State: open - Opened by maehler over 2 years ago

#108 - Bump numpy from 1.21.4 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 4 comments
Labels: dependencies

#107 - RNA junctions

Issue - State: open - Opened by dnil over 2 years ago

#106 - Add Changelog reminder

Issue - State: open - Opened by dnil over 2 years ago

#105 - Update mongo adapter for longer timeout

Pull Request - State: closed - Opened by dnil over 2 years ago - 2 comments

#104 - Deleting cases

Issue - State: open - Opened by ViktorHy over 2 years ago

#103 - Revert required version

Pull Request - State: closed - Opened by dnil over 2 years ago - 2 comments

#102 - Expand instructions on how to setup loqusdb and load a case

Pull Request - State: closed - Opened by northwestwitch over 2 years ago

#101 - Make a small tutorial for setting up a new database

Issue - State: closed - Opened by dnil over 2 years ago - 2 comments

#100 - fix revert script: set it

Pull Request - State: closed - Opened by dnil over 2 years ago - 2 comments

#99 - Revert contig name

Pull Request - State: closed - Opened by dnil over 2 years ago - 1 comment

#98 - Fix bnd

Pull Request - State: closed - Opened by J35P312 over 2 years ago

#97 - Export for interchromosomal variants broken

Issue - State: closed - Opened by dnil over 2 years ago - 1 comment
Labels: bug

#96 - Frequency by PASS/Fail flag

Issue - State: open - Opened by praveenraj2018 about 3 years ago

#95 - Bump pyyaml from 5.3.1 to 5.4

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies