loqusdb - Release 2.7.25

Merge pull request #167 from Clinical-Genomics/againupdatelock

Update poetry lock. Fix some issues with dependencies that dependabot…

- Python
Published by clingen-sthlm about 1 year ago

loqusdb - Release 2.7.24

Merge pull request #166 from Clinical-Genomics/deprecatedsetuptoolsresources

Fix #163 - avoid pkg_resources

- Python
Published by clingen-sthlm about 1 year ago

loqusdb - Release 2.7.23

Merge pull request #150 from Clinical-Genomics/docs_automation

update loqusdb docs

- Python
Published by clingen-sthlm about 1 year ago

loqusdb - Release 2.7.22

Update logic to better handle chromosome names during export (#159)

• update logic

• black

- Python
Published by clingen-sthlm about 1 year ago

loqusdb - Release 2.7.21

Update variant view command to check alternative chromosome representations (#158)

• check info with chr prefix and without it

• update changelog

• lint

• Update loqusdb/commands/view.py

Co-authored-by: Peter Pruisscher 57712924+peterpru@users.noreply.github.com

Co-authored-by: Peter Pruisscher 57712924+peterpru@users.noreply.github.com

- Python
Published by clingen-sthlm about 1 year ago

loqusdb - Release 2.7.20

add chrs for genome v38 (#156)

• add chrs for v38

• update tests

• changelog

• black format

• black format

• update docstrings

• update tests

- Python
Published by clingen-sthlm about 1 year ago

loqusdb - Release 2.7.19

Keep chr prefix when present (#157)

• keepchrprefix

• update changelog

• format black

• add tests

- Python
Published by clingen-sthlm about 1 year ago

loqusdb - Release 2.7.18

Ignore gq check if unset (#154)

• add an ignore-gq-if-unset flag

• update changelog

• update logic

• fix lint

• Update loqusdb/commands/load.py

Co-authored-by: Daniel Nilsson daniel.k.nilsson@gmail.com

Co-authored-by: Daniel Nilsson daniel.k.nilsson@gmail.com

- Python
Published by clingen-sthlm about 1 year ago

loqusdb - Release 2.7.17

Merge pull request #153 from Clinical-Genomics/fix-changelog-bump

fix changelog

- Python
Published by clingen-sthlm about 1 year ago

loqusdb - Release 2.7.16

Merge pull request #149 from Clinical-Genomics/fixchangelogagain

And again, fix changelog. That should hopefully be the last one.

- Python
Published by clingen-sthlm over 1 year ago

loqusdb - Release 2.7.14

Merge pull request #148 from Clinical-Genomics/fixbumpversionchangelog

Fix bumpversion changelog

- Python
Published by clingen-sthlm over 1 year ago

loqusdb - Release 2.7.13

Merge pull request #147 from Clinical-Genomics/keepachangelog

Bumpversion the changelog as well. Added changelog backlog.

- Python
Published by clingen-sthlm over 1 year ago

loqusdb - Release 2.7.12

Update the description of the Frq INFO tag (#144)

Changed

Update the description of the Frq INFO tag to include information about the number of cases as well.

- Python
Published by clingen-sthlm over 1 year ago

loqusdb - Release 2.7.11

Merge pull request #143 from Clinical-Genomics/add-linters

Changed

• Add linters

- Python
Published by clingen-sthlm almost 2 years ago

loqusdb - Release 2.7.10

Merge pull request #142 from Clinical-Genomics/add-codeowners

Changed

• Add codeowners

- Python
Published by clingen-sthlm almost 2 years ago

loqusdb - Release 2.7.9

Merge pull request #141 from Clinical-Genomics/fix-bump

Changed

-Fix bump action

- Python
Published by clingen-sthlm almost 2 years ago

loqusdb - Release 2.7.8

Merge pull request #137 from Clinical-Genomics/fix-bump-action

Changed

• Fix Bump action

- Python
Published by clingen-sthlm almost 2 years ago

loqusdb - Release 2.7.7

Merge pull request #133 from Clinical-Genomics/update_setuptools

Update setuptools to address a security issue

- Python
Published by clingen-sthlm almost 2 years ago

loqusdb - Release 2.7.6

Merge pull request #132 from Clinical-Genomics/dnil-patch-1

Update issue templates

- Python
Published by clingen-sthlm about 2 years ago

loqusdb - Release 2.7.5

Merge pull request #129 from Clinical-Genomics/optimise_index

Fix #127 - optimise index for sv queries

- Python
Published by clingen-sthlm over 2 years ago

loqusdb - Release 2.7.4

Merge pull request #131 from Clinical-Genomics/qual_dot

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

- Python
Published by clingen-sthlm over 2 years ago

loqusdb - Release 2.7.3

Merge pull request #124 from Clinical-Genomics/unfreeze_pymongo

Unfreeze PyMongo and replace deprecated count() with count_documents()

- Python
Published by clingen-sthlm over 2 years ago

loqusdb - Release 2.7.2

Merge pull request #123 from Clinical-Genomics/fixdeprecatedconfig

Fix installing error due to PyYaml version

- Python
Published by clingen-sthlm over 2 years ago

loqusdb - Release 2.7.1

Merge pull request #113 from Clinical-Genomics/dependabot/pip/setuptools-65.5.1

Bump setuptools from 59.2.0 to 65.5.1

- Python
Published by clingen-sthlm about 3 years ago

loqusdb - Release 2.7.0

Merge pull request #118 from Clinical-Genomics/qualgqfilter (minor)

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

- Python
Published by clingen-sthlm about 3 years ago

loqusdb - Release 2.6.10

Merge pull request #114 from Clinical-Genomics/fix/spelling-error

Fixed

• Spelling error of treshold to threshold

- Python
Published by clingen-sthlm over 3 years ago

loqusdb - Release 2.6.9

Merge pull request #105 from Clinical-Genomics/updatemongoadapter

Update mongo adapter for longer timeout

- Python
Published by clingen-sthlm about 4 years ago

loqusdb - Release 2.6.8

Merge pull request #103 from Clinical-Genomics/revertrequiredversion

Revert required version

- Python
Published by clingen-sthlm about 4 years ago

loqusdb - Release 2.6.7

Merge pull request #102 from Clinical-Genomics/tutorial

Expand instructions on how to setup loqusdb and load a case

- Python
Published by clingen-sthlm about 4 years ago

loqusdb - Release 2.6.6

Merge pull request #100 from Clinical-Genomics/fix_revert

fix revert script: set it

- Python
Published by clingen-sthlm about 4 years ago

loqusdb - Release 2.6.5

Merge pull request #99 from Clinical-Genomics/revertcontigname

Revert contig name

- Python
Published by clingen-sthlm about 4 years ago

loqusdb - Release 2.6.4

Merge pull request #98 from Clinical-Genomics/fix_BND

Fix bnd

- Python
Published by clingen-sthlm about 4 years ago

loqusdb - Release 2.6.3

Dependency on itself removed (patch)

- Python
Published by clingen-sthlm over 4 years ago

loqusdb - Release 2.6.2

Dependabot address pyyaml 5.4.0 (patch)

- Python
Published by clingen-sthlm over 4 years ago

loqusdb - Release 2.6.1

Lock dependency versions (#94) (patch)

Changed

• Lock dependency version

- Python
Published by clingen-sthlm over 4 years ago

loqusdb - Release 2.6.0

Support Bumpversion action #92 (minor)

- Python
Published by clingen-sthlm over 4 years ago

loqusdb - Github Actions

Use GitHub Actions for - running test - Submit coverage report to coveralls - publish release on pypi

- Python
Published by moonso about 5 years ago

loqusdb - Changelog + frequencies

Option to add observation frequencies to exported VCF (--freq)

- Python
Published by moonso about 5 years ago

loqusdb - Profiling

Added

• Profiling feature added. Each sample gets a profile based on the genotypes for a set of high maf variants.
• High maf variants used in profiling is loaded into DB via CLI
• Reject loading a case if a similar profile already exists for any of the samples
• Statistics of the profiles in DB can be generated through CLI
• use bulk operations when deleting variants
• Compatible with GRCh38
• Option to include case count when querying for a variant

Fixed

• Use correct fields in index

- Python
Published by moonso over 6 years ago

loqusdb - Use bulk upserts

Uses bulk operations to be more effective when inserting env variants

- Python
Published by moonso over 7 years ago

loqusdb - Annotate VCFs

loqus can annotate vcfs, both svs and SNVs from the command line

- Python
Published by moonso over 7 years ago

loqusdb - Introducing SVs

• Adds option to use SVs in loqusdb
• Adapts to Pymongo v 3.7

- Python
Published by moonso almost 8 years ago

loqusdb - Release 1.0

• Adds support for coordinates
• Allows for region searches
• Adds documentation

- Python
Published by moonso almost 9 years ago

loqusdb - Correct vcf header

- Python
Published by moonso about 9 years ago