Ecosyste.ms: Issues

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

GitHub / Clinical-Genomics/genmod issues and pull requests

#157 - Annotation update for chrM

Pull Request - State: closed - Opened by jemten 2 months ago

#155 - TODO on SV annotation - end looks odd

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

#154 - Lint issues

Issue - State: open - Opened by dnil 3 months ago
Labels: enhancement, QualityOfLife, Task

#153 - Add project toml and add uv to build

Pull Request - State: open - Opened by dnil 3 months ago - 7 comments

#152 - Fix sorting of variants

Pull Request - State: open - Opened by fellen31 3 months ago

#150 - Up to date GitHub pages documentation

Issue - State: open - Opened by fellen31 3 months ago
Labels: Documentation

#149 - genmod annotate - MT vs (chr)M

Issue - State: closed - Opened by fellen31 3 months ago - 1 comment
Labels: bug, question

#148 - Compounds only scores first family in VCF

Issue - State: open - Opened by fellen31 3 months ago - 2 comments

#146 - Is `--whole_gene` deprecated?

Issue - State: closed - Opened by fellen31 4 months ago - 2 comments

#144 - Fix #127 - update examples

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

#143 - Use uv

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

#142 - Release restriction on Python 3.8 (collections import)

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

#141 - Failing update pypi action - add as trusted repo on pypi

Issue - State: closed - Opened by dnil 4 months ago - 4 comments

#140 - Update readme

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

#139 - Bump version to 3.9

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

#138 - Add parameters for penalty and threshold

Pull Request - State: closed - Opened by Jakob37 4 months ago - 6 comments

#137 - Genmod compounds control threshold and assigned score

Issue - State: closed - Opened by Jakob37 4 months ago

#136 - Add GitHub Actions workflows for PyPI and CHANGELOG

Pull Request - State: closed - Opened by fellen31 5 months ago - 2 comments

#135 - Ensure chrX and X are treated equally

Pull Request - State: closed - Opened by fellen31 5 months ago - 1 comment

#134 - Fix unstable variants in models output

Pull Request - State: closed - Opened by fellen31 5 months ago

#133 - Unstable compounds order in output from genmod models

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

#132 - Model discrepancy when chrX has chr prefix (GRCh38)

Issue - State: closed - Opened by fellen31 6 months ago

#131 - Malformed INFO lines

Issue - State: closed - Opened by fellen31 6 months ago - 1 comment
Labels: enhancement

#130 - Scoring an empty VCF

Issue - State: open - Opened by fellen31 7 months ago
Labels: QualityOfLife

#129 - Create VCF_DRSahajal

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

#128 - Silently missing values when using integer format in rank model and encountering a float value

Issue - State: open - Opened by Jakob37 11 months ago - 2 comments
Labels: enhancement

#127 - "Error: No such option: -f" message when running example

Issue - State: closed - Opened by hrydbeck 11 months ago - 1 comment
Labels: Documentation

#126 - Phased models bugged?

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

#125 - Unfreeze python version, fix collections import

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

#124 - Makefile target for pypi dist upload

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

#123 - setup.py: Set version 3.8.2

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

#122 - Export Rankscore as Float Type

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

#121 - Mixed int-float in RankScore

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

#120 - setup.py: Lockdown genmod, limit compatibility to python v3.8

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

#119 - python3.10: import error

Issue - State: closed - Opened by jemten about 1 year ago - 1 comment

#119 - python3.10: import error

Issue - State: closed - Opened by jemten about 1 year ago - 1 comment

#118 - setup.py: Set version 3.8.1

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

#117 - setup py uplift requirements

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

#116 - TypeError: annotate() got an unexpected keyword argument 'regions'

Issue - State: closed - Opened by manburst over 1 year ago - 2 comments

#115 - container broken for version 3.8

Issue - State: closed - Opened by jemten over 1 year ago - 2 comments

#114 - CHANGELOG, setup.py changes for v3.8.0

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

#113 - Tag, build new release

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

#112 - Link to documentation broken

Issue - State: closed - Opened by Jakob37 over 1 year ago - 1 comment
Labels: bug

#111 - set abstract_sockets_supported to False

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

#110 - Compound scoring: Cap rankscore values to (min, ) range

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

#109 - requirements: Set fixed version for deps

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

#108 - Rankscore normalization

Pull Request - State: closed - Opened by torbjorgen almost 2 years ago - 11 comments

#107 - Change or document AR_compound low scoring compound penalty

Issue - State: open - Opened by dnil about 2 years ago - 4 comments
Labels: Task

#106 - Allow "Source" and "Version" in INFO header

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

#104 - Use poetry as build tool

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

#103 - Update docs on cli options

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

#102 - parse new header format

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

#101 - bug in parsing VCF header with filters that use escape character

Issue - State: closed - Opened by hassanfa about 4 years ago - 9 comments

#100 - Documentation for "strict" and "phased" seems to be broken

Issue - State: closed - Opened by bartcharbon about 4 years ago - 1 comment

#99 - Compound is missed if one parent is genotyped for each variant

Issue - State: open - Opened by bartcharbon about 4 years ago - 5 comments
Labels: bug

#98 - Genmod models '--vep' option throws exception

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

#97 - Incorrect "Compounds" INFO field in case of multiallelic records

Issue - State: closed - Opened by bartcharbon about 4 years ago - 2 comments

#96 - ANN standard format

Issue - State: open - Opened by dridk over 4 years ago
Labels: enhancement

#95 - Implement a tier based ranking for somatic mutations

Issue - State: open - Opened by hassanfa over 4 years ago - 3 comments
Labels: enhancement

#94 - no genetic model annotation

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

#93 - Some variants without GeneticModels annotation

Issue - State: closed - Opened by geocarvalho about 5 years ago - 1 comment

#92 - String matching in clinvar records..

Issue - State: closed - Opened by dnil over 5 years ago - 2 comments
Labels: duplicate, enhancement

#91 - GenMod error: 'list' object has no attribute 'split'

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

#90 - Incompatible CLI with click 7.0

Issue - State: closed - Opened by henrikstranneheim over 6 years ago
Labels: bug

#89 - Automatically determine pedigree?

Issue - State: closed - Opened by santiagorevale over 6 years ago - 1 comment

#88 - No "GeneticModels=" in the output

Issue - State: closed - Opened by jielab over 6 years ago - 2 comments

#86 - "record_rule = max" appears to prioritize based on max(value) rather than max(score)

Issue - State: open - Opened by bjhall over 6 years ago - 2 comments
Labels: Task

#85 - CSQ field is not parsed properly in genmod score when using --skip_plugin_check

Issue - State: open - Opened by hassanfa almost 7 years ago - 2 comments
Labels: Task

#84 - Food for thought: rank STR expansion variants?

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

#83 - Fixes indentation error in genetic_models

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

#82 - Compound error in 3.7.1 when single parent

Issue - State: closed - Opened by moonso over 7 years ago

#81 - Adds functionality to use reference files with chr prefix. Fix #66

Pull Request - State: closed - Opened by moonso about 8 years ago

#80 - Handle empty files

Pull Request - State: closed - Opened by moonso about 8 years ago

#79 - Compund score key error

Pull Request - State: closed - Opened by moonso about 8 years ago

#78 - does not work

Issue - State: closed - Opened by brianlamx about 8 years ago - 2 comments

#77 - Add build 38

Pull Request - State: closed - Opened by moonso about 8 years ago

#76 - No constraint on lenght in contig headers. Fix #73

Pull Request - State: closed - Opened by moonso about 8 years ago

#75 - Fix contig pattern

Pull Request - State: closed - Opened by moonso about 8 years ago - 1 comment

#74 - genmod build command does not work

Issue - State: closed - Opened by brianlamx about 8 years ago

#73 - Fix SyntaxError due to missing contig length for multisample VCF generated by Freebayes

Issue - State: closed - Opened by nilesh-tawari about 8 years ago - 1 comment
Labels: enhancement

#72 - Fix so that the program exits correct when there is a exception. Fix #53

Pull Request - State: closed - Opened by moonso about 8 years ago - 1 comment

#71 - Allow smaller queue to avoid memory problems for multiprocessing

Pull Request - State: closed - Opened by moonso about 8 years ago

#70 - Fix key error

Pull Request - State: closed - Opened by moonso about 8 years ago

#69 - Modify rank model for reduced penetrance genes

Issue - State: open - Opened by henrikstranneheim about 8 years ago - 1 comment
Labels: Under discussion

#68 - Adds lacking csq information when scoring

Pull Request - State: closed - Opened by moonso over 8 years ago

#67 - vcf_extractor fails to find VEP format for CSQ score model?

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

#66 - Can not handle when chromosome prefix differs in vcf and resource

Issue - State: closed - Opened by moonso over 8 years ago - 2 comments

#65 - VEP Friendly Output

Issue - State: closed - Opened by AndrewSkelton over 8 years ago - 2 comments

#64 - Ped File

Issue - State: closed - Opened by AndrewSkelton over 8 years ago - 5 comments

#63 - Problem with encodings

Issue - State: closed - Opened by moonso almost 9 years ago

#62 - handle about the GATKHardSNP in VCF header

Issue - State: closed - Opened by hmkim almost 9 years ago - 2 comments

#61 - Add support for IMPRECISE variants when querying a ref vcf

Issue - State: open - Opened by henrikstranneheim almost 9 years ago
Labels: enhancement

#60 - error with interval-tree

Issue - State: closed - Opened by mkohram almost 9 years ago - 5 comments