Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / Clinical-Genomics/stranger issues and pull requests

#84 - UnboundLocalError when decomposing multiallelic variants

Issue - State: open - Opened by Schmytzi about 1 month ago

#82 - Fix #81 - setuptools not explicit in all distros - switch to uv

Pull Request - State: open - Opened by dnil 3 months ago - 2 comments

#81 - Fix setup tools compatibility issues

Issue - State: open - Opened by dnil 3 months ago

#80 - Non-reference expansion pathogenic alleles (LRS in particular)

Issue - State: open - Opened by dnil 4 months ago - 1 comment
Labels: enhancement

#79 - Version 0.9.2 - fix output of multi individual format and unannotated loci

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

#78 - Fix #76 - revert to output unannotated loci

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

#77 - Fix #73 - out format for multiindividuals decompose

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

#76 - Different output for repeats with missing info

Issue - State: closed - Opened by Stikus 5 months ago - 4 comments

#75 - Fix coverage upload hidden artifact new required option

Pull Request - State: closed - Opened by dnil 5 months ago - 1 comment

#74 - provide annotations for Straglr VCF

Issue - State: open - Opened by anuravi1234 5 months ago - 1 comment
Labels: question

#73 - Annotate multi-sample VCF

Issue - State: closed - Opened by fellen31 7 months ago - 5 comments

#72 - Add test for trgt

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

#71 - Add test for when TRGT `FORMAT.MC` is `.`

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

#70 - scout link

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

#69 - swap coveralls image for codecov

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

#68 - Release 0.9.1 - TRGT missing MC fallback fix

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

#67 - Fix #48 - add GitHub Actions workflows

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

#66 - Rename MASTER to MAIN

Issue - State: closed - Opened by dnil 7 months ago - 1 comment

#65 - Update docs trgt

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

#64 - Fix #63 - fallback if MC is .

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

#63 - Invalid literal for int() with base 10: '.'

Issue - State: closed - Opened by fellen31 8 months ago - 3 comments

#62 - Bump version to 0.9

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

#61 - Pathologic motif pos for RFC1, RAPGEF2

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

#60 - Add STRdust

Pull Request - State: open - Opened by fellen31 9 months ago

#59 - Small fixes for TRGT

Pull Request - State: closed - Opened by fellen31 9 months ago - 3 comments

#58 - Add missing useful keys from ExHu

Issue - State: closed - Opened by dnil 9 months ago - 1 comment

#57 - Matching inheritance pattern annotation

Issue - State: open - Opened by dnil 10 months ago
Labels: enhancement

#56 - Update docs for TRGT mode

Issue - State: closed - Opened by dnil 10 months ago

#53 - afterthought: typo pathogenic

Pull Request - State: closed - Opened by dnil 10 months ago

#52 - Parse trgt entries - FORMAT.MC in practice - also if VCF not split

Pull Request - State: closed - Opened by dnil 10 months ago - 2 comments

#51 - decompose TRGT VCF

Issue - State: closed - Opened by dnil 11 months ago

#50 - Variant catalog update hg38

Issue - State: closed - Opened by cogrho 11 months ago - 2 comments

#49 - Fix #47 - bring in updated references to demo

Pull Request - State: closed - Opened by dnil 12 months ago - 1 comment

#48 - Add GitHub Actions automation for tests etc instead of Travis-CI

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

#47 - Add novel repeat expansions

Issue - State: closed - Opened by bopohdr about 1 year ago - 4 comments

#46 - Adapt for TRGT output

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

#45 - (up) add docker image

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

#44 - Release 0.8.1 missing?

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

#43 - V0.8.1

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

#42 - Variant catalog and DAB1

Issue - State: closed - Opened by A97paupic over 3 years ago - 1 comment

#41 - POLG hg38 coordinates

Issue - State: closed - Opened by bw2 over 3 years ago - 2 comments

#40 - Warnings thrown

Issue - State: closed - Opened by ViktorHy over 3 years ago - 2 comments

#39 - V0.8.0

Pull Request - State: closed - Opened by dnil over 3 years ago

#38 - Fix #37, Fix #36 and some additional potential obis.

Pull Request - State: closed - Opened by dnil over 3 years ago

#37 - Review HGNCId - LocusId associations

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

#36 - different attributes in GRCh37 vs. GRCh38 catalogs

Issue - State: closed - Opened by bw2 over 3 years ago - 2 comments

#35 - Fix #33 Fix #34 - GLS, RFC1 hg19 obi1

Pull Request - State: closed - Opened by dnil over 3 years ago

#34 - RFC1 ReferenceRegion for GRCh37

Issue - State: closed - Opened by bw2 over 3 years ago - 1 comment

#33 - GLS ReferenceRegion for GRCh37

Issue - State: closed - Opened by bw2 over 3 years ago - 1 comment

#32 - Bean link

Pull Request - State: closed - Opened by dnil almost 4 years ago

#31 - Update README..

Pull Request - State: closed - Opened by dnil almost 4 years ago

#30 - Bump version to 0.7.1

Pull Request - State: closed - Opened by dnil almost 4 years ago

#29 - Update rank score model

Pull Request - State: closed - Opened by dnil almost 4 years ago

#28 - Add family_id CLI option

Pull Request - State: closed - Opened by dnil about 4 years ago - 5 comments

#27 - Update variant_catalog for hg38

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

#26 - Added new variants and tags. Fix #21. Fix #22. Fix #23. Fix #24. Prep…

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

#25 - Add rarity statistic from normal population

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

#24 - Other genes

Issue - State: closed - Opened by dnil over 4 years ago - 2 comments

#23 - Source

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

#22 - Ensure applicable HGNC-ids / symbols

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

#21 - Introduce new meta-data columns

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

#20 - Update docs

Issue - State: closed - Opened by dnil about 5 years ago

#19 - Release 0.5.6 - naive rank score.

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

#18 - Fix #14: add a naive rank score.

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

#17 - Bumps version to 0.5.5

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

#16 - Fix #15 - Sync variant catalog w exhu3.1.2 and MIP8 refs.

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

#15 - Add limits also for NIPA1 and NOTCH2NL

Issue - State: closed - Opened by dnil about 5 years ago

#14 - Rank model for stranger

Issue - State: closed - Opened by dnil about 5 years ago

#13 - Add the normal/pathogenic limits for each variant to the VCF

Pull Request - State: closed - Opened by bjhall over 5 years ago - 4 comments

#12 - Add GLS, RFC1 to variant catalog (and harmonize).

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

#11 - RFC1, GLS definitions

Issue - State: closed - Opened by dnil over 5 years ago - 1 comment

#10 - Update manifest - and bump version again.

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

#9 - Both repid json def

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

#8 - Attempt to use both kinds of ExHu REPID naming

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

#7 - make json file default rep file, and include in dict

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

#6 - REPID changed again in EH v3.0.0 release?!

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

#5 - Add refs field to json file

Issue - State: closed - Opened by moonso about 6 years ago - 5 comments

#4 - Catalog POLG, DIP2B. Fix exhu3 repid.

Pull Request - State: closed - Opened by dnil about 6 years ago - 2 comments

#3 - Exhu 3.0

Pull Request - State: closed - Opened by moonso about 6 years ago - 1 comment

#2 - ExpansionHunter v3.0.0-rc1

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

#1 - Expanded expansions loci file.

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