Ecosyste.ms: Issues

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GitHub / Clinical-Genomics/loqusdb issues and pull requests

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

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

#130 - No frequencies shown for mitochondrial variants

Issue - State: open - Opened by Jakob37 6 months ago
Labels: question

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

Pull Request - State: closed - Opened by dnil 7 months ago - 7 comments

#128 - Handle TIDDIT style SV type names

Pull Request - State: open - Opened by dnil 7 months ago

#127 - Improve indexes

Issue - State: closed - Opened by northwestwitch 8 months ago
Labels: enhancement

#126 - index missing on loqusdb-tumor

Issue - State: closed - Opened by dnil 8 months ago - 2 comments

#125 - Bump pip from 23.1.2 to 23.3

Pull Request - State: open - Opened by dependabot[bot] 8 months ago
Labels: dependencies

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

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 3 comments

#123 - Fix installing error due to PyYaml version

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 6 comments

#122 - Deprecated config in `setup.cfg`

Issue - State: closed - Opened by northwestwitch 9 months ago - 1 comment
Labels: bug

#121 - unfreeze PyMongo

Issue - State: closed - Opened by northwestwitch 9 months ago - 2 comments
Labels: enhancement

#120 - Mei variant

Pull Request - State: open - Opened by dnil 9 months ago

#119 - Store MEI variants

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

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

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

#117 - Use QUAL for filtering in addition to GQ

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

#115 - log homozygous families

Issue - State: open - Opened by dnil over 1 year ago - 4 comments

#114 - fix(treshold -> threshold)

Pull Request - State: closed - Opened by karlnyr over 1 year ago - 2 comments

#113 - Bump setuptools from 59.2.0 to 65.5.1

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

#112 - Loqusdb upload SV variant type

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

#111 - Option to select individual for upload

Pull Request - State: open - Opened by dnil over 1 year ago - 2 comments

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

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

#108 - Bump numpy from 1.21.4 to 1.22.0

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

#107 - RNA junctions

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

#106 - Add Changelog reminder

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

#105 - Update mongo adapter for longer timeout

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

#104 - Deleting cases

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

#103 - Revert required version

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

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

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

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

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

#100 - fix revert script: set it

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

#99 - Revert contig name

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

#98 - Fix bnd

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

#97 - Export for interchromosomal variants broken

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

#96 - Frequency by PASS/Fail flag

Issue - State: open - Opened by praveenraj2018 over 2 years ago

#95 - Bump pyyaml from 5.3.1 to 5.4

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

#94 - Lock dependency versions

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

#93 - Freeze PyMongo to version < 4.0

Issue - State: closed - Opened by northwestwitch over 2 years ago - 1 comment

#92 - Add hobbit action

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

#91 - isort

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

#90 - black

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

#89 - Removed changelog action

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

#88 - Isort and black

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

#87 - Reformat with black and isort

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

#86 - Use newer cyvcf

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

#84 - Option to connect to MongoDB replica set instead of standalone databases

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

#83 - Adds a workflow for testing and coverage on github actions

Pull Request - State: closed - Opened by moonso about 3 years ago

#82 - Bumps version to 2.5.1

Pull Request - State: closed - Opened by moonso about 3 years ago

#81 - Create CONTRIBUTING.md

Pull Request - State: closed - Opened by henrikstranneheim about 3 years ago

#80 - feat(pypi): Via github actions

Pull Request - State: closed - Opened by henrikstranneheim about 3 years ago

#79 - RESTapi for containerization

Issue - State: closed - Opened by mhkc over 3 years ago - 7 comments

#78 - Updates README to document config file

Pull Request - State: closed - Opened by moonso about 4 years ago

#77 - Add observation frequency to every variant of the exported VCF

Pull Request - State: closed - Opened by bjhall about 4 years ago - 3 comments

#76 - REST interface

Issue - State: closed - Opened by dnil over 4 years ago - 3 comments

#75 - Remove logs when searching SVs

Pull Request - State: closed - Opened by adrosenbaum over 4 years ago

#74 - frequency and count tag for the variant clusters

Issue - State: open - Opened by J35P312 over 4 years ago

#73 - Case count

Pull Request - State: closed - Opened by moonso over 4 years ago - 1 comment

#72 - Updates coordinates index. Fix #71

Pull Request - State: closed - Opened by moonso over 4 years ago

#71 - Index on non-existing key

Issue - State: closed - Opened by adrosenbaum over 4 years ago - 1 comment

#70 - Fix variant sorting when exporting

Pull Request - State: closed - Opened by adrosenbaum over 4 years ago - 3 comments

#69 - Add support for genome build 38

Pull Request - State: closed - Opened by adrosenbaum over 4 years ago - 4 comments

#68 - Modifying SV counting

Pull Request - State: closed - Opened by sjurug almost 5 years ago - 4 comments

#67 - This PR tries to solve several issues regarding the 'delete' feature in loqusdb

Pull Request - State: closed - Opened by adrosenbaum almost 5 years ago - 3 comments

#66 - Missing context on delete

Issue - State: closed - Opened by adrosenbaum almost 5 years ago

#65 - Lift MAF snp profile to grch38

Issue - State: open - Opened by henrikstranneheim almost 5 years ago

#64 - Dealing with setting end = float('inf')

Pull Request - State: closed - Opened by adrosenbaum about 5 years ago

#63 - Add option to check for duplicates

Pull Request - State: closed - Opened by adrosenbaum about 5 years ago

#62 - Make profiling feature compatible with a loqusdb-v1 database.

Pull Request - State: closed - Opened by adrosenbaum about 5 years ago - 2 comments

#61 - Sample profiling

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 10 comments

#60 - Update cli behaviour

Pull Request - State: closed - Opened by moonso over 5 years ago

#59 - Allows usage of config to connect to database. Fix #58

Pull Request - State: closed - Opened by moonso over 5 years ago

#58 - Use config to connect to database

Issue - State: closed - Opened by moonso over 5 years ago

#57 - Exists with non zero if case does not exist in loqusdb cases command

Pull Request - State: closed - Opened by moonso over 5 years ago

#56 - Use bulk insert

Pull Request - State: closed - Opened by moonso over 5 years ago

#55 - Gzipped issue

Pull Request - State: closed - Opened by moonso over 5 years ago

#54 - unnable to find gzipped file

Issue - State: closed - Opened by J35P312 over 5 years ago

#53 - Fix deps for version 1.0

Issue - State: closed - Opened by moonso over 5 years ago

#52 - Annotate vcf

Pull Request - State: closed - Opened by moonso almost 6 years ago

#51 - Pymongo version

Pull Request - State: closed - Opened by barrystokman almost 6 years ago

#50 - Version 2.0

Pull Request - State: closed - Opened by moonso almost 6 years ago

#49 - Funky install error

Issue - State: closed - Opened by J35P312 almost 6 years ago - 1 comment

#48 - Houston, we have a problem!

Issue - State: closed - Opened by J35P312 almost 6 years ago - 2 comments

#47 - require cyvcf2 to be less than 0.10.0

Pull Request - State: closed - Opened by patrikgrenfeldt almost 6 years ago - 1 comment

#46 - Lock pymongo to the same version as scout-browser

Pull Request - State: closed - Opened by ingkebil almost 6 years ago - 1 comment

#45 - Add sv

Pull Request - State: closed - Opened by moonso almost 6 years ago

#44 - Create VCF export of structural variants

Issue - State: closed - Opened by moonso almost 6 years ago

#43 - Freeze cyvcf2 to latest known compatible version

Issue - State: closed - Opened by patrikgrenfeldt almost 6 years ago - 1 comment

#42 - release 1.0 logs wrong connection string

Issue - State: closed - Opened by ingkebil about 6 years ago - 4 comments

#41 - Expand documentation

Issue - State: open - Opened by moonso about 6 years ago - 1 comment

#40 - fixed the end_chromosome problem

Pull Request - State: closed - Opened by J35P312 about 6 years ago - 4 comments

#39 - --end-chromosome is not used

Issue - State: closed - Opened by J35P312 about 6 years ago - 1 comment

#38 - Add sv

Pull Request - State: closed - Opened by J35P312 about 6 years ago

#37 - Sort positions when storing/querying bnd

Issue - State: closed - Opened by J35P312 about 6 years ago - 3 comments

#36 - frequency annotation of a vcf file

Issue - State: closed - Opened by J35P312 about 6 years ago - 2 comments

#35 - Import Database

Issue - State: open - Opened by J35P312 about 6 years ago - 4 comments

#34 - Allow interval size to be a parameter

Issue - State: open - Opened by moonso over 6 years ago

#33 - Add sv

Pull Request - State: closed - Opened by moonso over 6 years ago

#32 - Migrate

Pull Request - State: closed - Opened by moonso almost 7 years ago