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
#118 - setup.py: Set version 3.8.1
Pull Request -
State: closed - Opened by torbjorgen 11 months ago
#117 - setup py uplift requirements
Pull Request -
State: closed - Opened by torbjorgen 11 months ago
- 2 comments
#116 - TypeError: annotate() got an unexpected keyword argument 'regions'
Issue -
State: open - Opened by manburst 11 months ago
#115 - container broken for version 3.8
Issue -
State: closed - Opened by jemten 11 months ago
- 2 comments
#114 - CHANGELOG, setup.py changes for v3.8.0
Pull Request -
State: closed - Opened by torbjorgen 12 months ago
- 1 comment
#113 - Tag, build new release
Issue -
State: closed - Opened by torbjorgen 12 months ago
#112 - Link to documentation broken
Issue -
State: open - Opened by Jakob37 about 1 year ago
#111 - set abstract_sockets_supported to False
Pull Request -
State: closed - Opened by ramprasadn about 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 over 1 year ago
- 11 comments
#107 - Change or document AR_compound low scoring compound penalty
Issue -
State: open - Opened by dnil almost 2 years ago
#106 - Allow "Source" and "Version" in INFO header
Pull Request -
State: open - Opened by maehler over 2 years ago
#105 - Error occurs if one or more variants in vep annotated VCF lacks VEP annotation when running with --vep
Issue -
State: open - Opened by bartcharbon over 3 years ago
- 1 comment
#104 - Use poetry as build tool
Pull Request -
State: open - Opened by moonso over 3 years ago
#103 - Update docs on cli options
Pull Request -
State: closed - Opened by moonso over 3 years ago
#102 - parse new header format
Pull Request -
State: closed - Opened by moonso over 3 years ago
#101 - bug in parsing VCF header with filters that use escape character
Issue -
State: closed - Opened by hassanfa over 3 years ago
- 9 comments
#100 - Documentation for "strict" and "phased" seems to be broken
Issue -
State: closed - Opened by bartcharbon over 3 years ago
- 1 comment
#99 - Compound is missed if one parent is genotyped for each variant
Issue -
State: open - Opened by bartcharbon over 3 years ago
- 4 comments
#98 - Genmod models '--vep' option throws exception
Issue -
State: closed - Opened by bartcharbon over 3 years ago
- 6 comments
#97 - Incorrect "Compounds" INFO field in case of multiallelic records
Issue -
State: closed - Opened by bartcharbon almost 4 years ago
- 2 comments
#96 - ANN standard format
Issue -
State: open - Opened by dridk about 4 years ago
#95 - Implement a tier based ranking for somatic mutations
Issue -
State: open - Opened by hassanfa over 4 years ago
- 2 comments
#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 almost 5 years ago
- 1 comment
#92 - String matching in clinvar records..
Issue -
State: open - Opened by dnil almost 5 years ago
#91 - GenMod error: 'list' object has no attribute 'split'
Issue -
State: closed - Opened by fgvieira about 5 years ago
- 1 comment
#90 - Incompatible CLI with click 7.0
Issue -
State: closed - Opened by henrikstranneheim almost 6 years ago
Labels: bug
#89 - Automatically determine pedigree?
Issue -
State: closed - Opened by santiagorevale about 6 years ago
- 1 comment
#88 - No "GeneticModels=" in the output
Issue -
State: closed - Opened by jielab about 6 years ago
- 2 comments
#87 - genmod score, data_type=string appears to match when the rule is a substring of the string in the VCF
Issue -
State: open - Opened by bjhall over 6 years ago
#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
- 1 comment
#85 - CSQ field is not parsed properly in genmod score when using --skip_plugin_check
Issue -
State: open - Opened by hassanfa over 6 years ago
#84 - Food for thought: rank STR expansion variants?
Issue -
State: closed - Opened by dnil over 6 years ago
- 1 comment
#83 - Fixes indentation error in genetic_models
Pull Request -
State: closed - Opened by moonso about 7 years ago
#82 - Compound error in 3.7.1 when single parent
Issue -
State: closed - Opened by moonso about 7 years ago
#81 - Adds functionality to use reference files with chr prefix. Fix #66
Pull Request -
State: closed - Opened by moonso over 7 years ago
#80 - Handle empty files
Pull Request -
State: closed - Opened by moonso over 7 years ago
#79 - Compund score key error
Pull Request -
State: closed - Opened by moonso over 7 years ago
#78 - does not work
Issue -
State: closed - Opened by brianlamx over 7 years ago
- 2 comments
#77 - Add build 38
Pull Request -
State: closed - Opened by moonso over 7 years ago
#76 - No constraint on lenght in contig headers. Fix #73
Pull Request -
State: closed - Opened by moonso over 7 years ago
#75 - Fix contig pattern
Pull Request -
State: open - Opened by moonso over 7 years ago
#74 - genmod build command does not work
Issue -
State: closed - Opened by brianlamx over 7 years ago
#73 - Fix SyntaxError due to missing contig length for multisample VCF generated by Freebayes
Issue -
State: closed - Opened by nilesh-tawari over 7 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 over 7 years ago
- 1 comment
#71 - Allow smaller queue to avoid memory problems for multiprocessing
Pull Request -
State: closed - Opened by moonso almost 8 years ago
#70 - Fix key error
Pull Request -
State: closed - Opened by moonso almost 8 years ago
#69 - Modify rank model for reduced penetrance genes
Issue -
State: open - Opened by henrikstranneheim almost 8 years ago
#68 - Adds lacking csq information when scoring
Pull Request -
State: closed - Opened by moonso almost 8 years ago
#67 - vcf_extractor fails to find VEP format for CSQ score model?
Issue -
State: closed - Opened by dnil about 8 years ago
- 2 comments
#66 - Can not handle when chromosome prefix differs in vcf and resource
Issue -
State: closed - Opened by moonso about 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 over 8 years ago
#62 - handle about the GATKHardSNP in VCF header
Issue -
State: closed - Opened by hmkim over 8 years ago
- 2 comments
#61 - Add support for IMPRECISE variants when querying a ref vcf
Issue -
State: open - Opened by henrikstranneheim over 8 years ago
Labels: enhancement
#60 - error with interval-tree
Issue -
State: closed - Opened by mkohram over 8 years ago
- 5 comments
#59 - Added option temp_dir. Fix #58
Pull Request -
State: closed - Opened by moonso over 8 years ago
#58 - GENMOD on bigger VCF file - IO Error
Issue -
State: closed - Opened by tinuthomas over 8 years ago
- 3 comments
#57 - Handle no affected
Pull Request -
State: closed - Opened by moonso over 8 years ago
#56 - Skip families without affected
Issue -
State: closed - Opened by moonso over 8 years ago
#55 - GENMOD output gives pattern of inheritance for familes with no genotype data
Issue -
State: closed - Opened by tinuthomas over 8 years ago
- 5 comments
#54 - Genmod writes ExAC_MAX_AF to vcf header when using --thousand_g
Issue -
State: closed - Opened by henrikstranneheim over 8 years ago
#53 - Catch error and make clean exit
Issue -
State: closed - Opened by henrikstranneheim over 8 years ago
#52 - Fixed problem with sv alt fields. Added tests
Pull Request -
State: closed - Opened by moonso over 8 years ago
#51 - Problem with SV alt fields
Issue -
State: closed - Opened by moonso over 8 years ago
#50 - Add COSMIC annotation
Issue -
State: closed - Opened by moonso over 8 years ago
#49 - Build Wiki
Issue -
State: closed - Opened by AndrewSkelton over 8 years ago
- 4 comments
#48 - Feature/compound problems
Pull Request -
State: closed - Opened by moonso over 8 years ago
#47 - Problem with compounds when splitted with vt
Issue -
State: closed - Opened by moonso over 8 years ago
#46 - installation issues ?
Issue -
State: closed - Opened by parlar over 8 years ago
- 5 comments
#45 - Add support to extract RS number, and MAX_AF from 1000G annotation as new info keys in vcf
Issue -
State: closed - Opened by henrikstranneheim over 8 years ago
#44 - Add support for MT inheritance models
Issue -
State: open - Opened by henrikstranneheim almost 9 years ago
- 3 comments
#43 - Annotating with CADD Scores
Issue -
State: closed - Opened by lukewbonham almost 9 years ago
- 12 comments
#42 - Problem with high GQ
Issue -
State: closed - Opened by moonso about 9 years ago
#41 - Reducing AR_comp model noise
Issue -
State: closed - Opened by dnil about 9 years ago
- 3 comments
#40 - Modify geneticModels based on reduced penetrance for supplied genes
Issue -
State: closed - Opened by henrikstranneheim about 9 years ago
- 3 comments
#39 - New SO-terms
Issue -
State: closed - Opened by moonso about 9 years ago
#38 - Problems with genmod score
Issue -
State: closed - Opened by emmser over 9 years ago
#37 - Missing compounds
Issue -
State: closed - Opened by robinandeer over 9 years ago
- 11 comments
#36 - 'generate_pairs' is not defined
Issue -
State: closed - Opened by wclee47 over 9 years ago
- 2 comments
#35 - KeyError: u'genmod/configs/rank_model_test_v1.4.ini'
Issue -
State: closed - Opened by wclee47 over 9 years ago
- 5 comments
#34 - Annotating with CADD
Issue -
State: closed - Opened by landyk01 almost 10 years ago
- 4 comments
#33 - Annotate with CADD not working
Issue -
State: closed - Opened by landyk01 almost 10 years ago
- 1 comment
#32 - Update build_annotation.py
Pull Request -
State: closed - Opened by glabilloy almost 10 years ago
- 1 comment
#31 - Question for X-Linked recessive case analysis
Issue -
State: closed - Opened by hmkim almost 10 years ago
- 4 comments
#30 - Does this work for VCFs with more than one trio?
Issue -
State: closed - Opened by leipzig almost 10 years ago
- 6 comments
#29 - genmod breaking VCF format when adding software tag to header
Issue -
State: closed - Opened by tzhughes almost 10 years ago
- 2 comments
#28 - Sort order not respected by genmod
Issue -
State: closed - Opened by tzhughes almost 10 years ago
- 3 comments
#27 - Analysing WG quad data- genmod
Issue -
State: closed - Opened by tzhughes almost 10 years ago
- 29 comments
#26 - Version 1.5.19 crashing also with test data but with different error
Issue -
State: closed - Opened by tzhughes almost 10 years ago
- 2 comments
#25 - Version 1.5.19 crashing
Issue -
State: closed - Opened by tzhughes almost 10 years ago
- 2 comments
#24 - Implement genmod analyze
Issue -
State: closed - Opened by moonso over 10 years ago
- 1 comment
#23 - Add -strict flag
Issue -
State: closed - Opened by moonso over 10 years ago
- 1 comment
#22 - change to relative imports within package
Issue -
State: closed - Opened by moonso over 10 years ago
#21 - AR_comp design
Issue -
State: closed - Opened by tzhughes over 10 years ago
- 16 comments
#20 - Denovo and noCalls
Issue -
State: closed - Opened by tzhughes over 10 years ago
- 9 comments
#19 - Stats from real data indicate that implementation of -phase is a loosening of conditions
Issue -
State: closed - Opened by tzhughes over 10 years ago
- 32 comments