Ecosyste.ms: Issues

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

GitHub / oxfordmmm/gnomonicus issues and pull requests

#91 - bump: piezo 0.9.1

Pull Request - State: closed - Opened by JeremyWesthead 5 days ago

#90 - fix: grumpy 0.2.5

Pull Request - State: closed - Opened by JeremyWesthead about 2 months ago

#89 - Fix/produce empty effects csv

Pull Request - State: closed - Opened by JeremyWesthead about 2 months ago - 2 comments

#88 - fix: grumpy 0.2.4

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

#87 - fix: use piezo 0.9.0

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

#86 - Bump/grumpy 0.2.2

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

#85 - bump: vcf_subset 2.0.0

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

#84 - Feat/use grumpy

Pull Request - State: closed - Opened by JeremyWesthead 6 months ago

#83 - fix: gumpy 1.3.8

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

#82 - fix: gumpy 1.3.7

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

#81 - fix: gumpy 1.3.6

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

#80 - fix: use piezo 0.8.4

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

#79 - fix: use gumpy 1.3.5

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

#78 - fix: if a gvcf row has a COV field, don't use DP

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

#77 - bump: version++

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

#76 - fix: bump gumpy to allow vcf overlaps

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

#75 - bump: gumpy 1.3.3

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

#74 - bump: use gumpy 1.3.2

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago

#73 - fix: make sure duplicate rows can't make it through

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago

#72 - bump: vcf_subset 1.1.2

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago

#71 - bump: version++

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago

#70 - bump: gumpy 1.3.1

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago

#69 - fix: ensure all minos positions from merge-vcfs

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago

#68 - Feat/gvcf support

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago

#67 - bump: version to 2.5.7

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago

#66 - Fix/dont fasta adjudicate deletions

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago

#65 - fix: bump version

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

#64 - fix: order variants better

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

#63 - fix: ensure docker build runs

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

#62 - fix: bump version for release

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

#61 - fix: ensure that fasta adjudication happens, even in cases of 0 mutat…

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

#60 - Fix/sort json

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

#58 - fix: bump gumpy version

Pull Request - State: closed - Opened by JeremyWesthead 11 months ago

#57 - fix: bump piezo version

Pull Request - State: closed - Opened by JeremyWesthead 11 months ago

#56 - Feat/epistasis support

Pull Request - State: closed - Opened by JeremyWesthead 11 months ago

#55 - fix(update-table): ensure append on outputDir

Pull Request - State: closed - Opened by JeremyWesthead 12 months ago

#54 - VERSION++

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

#53 - Feat/table update script

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

#52 - fix: ensure fasta adjudicated mutations get all predictions

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

#51 - tuberculosis amr catalogues

Issue - State: closed - Opened by alantsangmb about 1 year ago - 5 comments

#50 - fix: use gumpy 1.2.6

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

#49 - Fix/gzip python3.12

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

#48 - Fix/avoid duplicate rrs

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

#47 - Fix/fasta adj evidence

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

#46 - Return gene position for fasta nucleotide nulls

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

#42 - Feat/fasta adjudication

Pull Request - State: open - Opened by JeremyWesthead over 1 year ago

#41 - Feat/add evidence

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

#39 - Fix to use `None` values if vcf idx cannot be found (#36)

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

#38 - Fix to ensure that multis aren't erroneously duplicated

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

#37 - "All arrays must be of the same length"

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

#35 - Added error handling to temporarily appease oxfordmmm/gumpy#24

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

#34 - `gene_name` --> `gene` in variants.csv for #33

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

#33 - `gene` is called `gene_name` in `variants`

Issue - State: open - Opened by philipwfowler over 1 year ago - 1 comment

#32 - Added s3fs req

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

#30 - Added pushing to OCR as well as dockerhub for GPAS

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

#29 - Add version flag

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

#28 - OutdatedGumpyException

Issue - State: closed - Opened by alantsangmb over 1 year ago - 3 comments

#27 - gnomonicus version

Issue - State: closed - Opened by alantsangmb over 1 year ago - 5 comments

#26 - minor alleles incorrectly classified as dominant for `1/1` calls

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

#25 - Fix for minor indel nc changes

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

#24 - Fix for #22

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

#23 - VCF edge case: `TypeError: 'NoneType' object is not subscriptable`

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

#22 - edge case when VCF contains no valid rows

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

#21 - Ensure all values are properly converted to null

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

#20 - Bug fixes

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

#18 - fails if a minor allele has equal numbers of reads in REF and ALT

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

#17 - Fix pickled genome issue

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

#15 - Minor aa fixes

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

#14 - Cicd docs

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

#13 - insertions in reverse complement genes

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

#12 - Large deletions

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

#11 - fails to parse detected minor population mutant

Issue - State: closed - Opened by philipwfowler almost 2 years ago - 5 comments

#10 - Explictly type cast pandas DataFrames to avoid FutureWarnings

Pull Request - State: closed - Opened by JeremyWesthead almost 2 years ago

#9 - Add minor index parsing to the CLI script + various pandas index fixes

Pull Request - State: closed - Opened by JeremyWesthead almost 2 years ago

#8 - Fixed minority populations. Added extra tests for these

Pull Request - State: closed - Opened by JeremyWesthead almost 2 years ago - 1 comment

#7 - Various improvements to tests. Now at 100% coverage

Pull Request - State: closed - Opened by JeremyWesthead almost 2 years ago

#6 - InvalidMutationException

Issue - State: closed - Opened by alantsangmb about 2 years ago - 7 comments

#5 - No entry found in the catalogue

Issue - State: closed - Opened by alantsangmb about 2 years ago - 9 comments

#4 - Dev

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

#3 - Rollback python 3.9

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

#2 - Added fasta file generation flag to the CLI for user story 3

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

#1 - To json

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