Ecosyste.ms: Issues

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GitHub / oxfordmmm/gumpy issues and pull requests

#40 - fix: check for None on filter before `in` check

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

#39 - fix: expand which filters are allowed for nulls and minor alleles

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

#38 - Allow multiple filters

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

#37 - fix: ensure null calls make it through filter fails

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

#36 - Fix/allow vcf row overlap

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

#35 - Fix/allow vcf row overlap

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

#34 - Fix/null deletion edge case

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago - 2 comments

#33 - fix: remove erroneous print

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

#32 - feat: added logic for GVCF rows

Pull Request - State: closed - Opened by JeremyWesthead 8 months ago - 1 comment

#31 - fix: check clashes within get_calls

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

#30 - Allow AD instead of COV for minor populations

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

#29 - Additions to enable type checking of this as an import

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

#28 - Style/black ruff

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

#27 - fix: Fix for oxfordmmm/gnomonicus#37

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

#26 - fix: ensure minor populations aren't searched for in null calls

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

#25 - Added fix for oxfordmmm/gnomonicus#31

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

#24 - IndexError when processing CRyPTIC samples

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

#23 - Fix for `gnomonicus` issue

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

#22 - Fix to minor indel nc changes

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

#21 - Vcf fix

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

#20 - Vcf fix

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

#19 - Fixes for pulling out gene positions of large dels crossing genes

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

#18 - Various fixes/improvements including minor AAs

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

#17 - Conflicting indels starting at a given position cause crashes

Issue - State: open - Opened by JeremyWesthead over 1 year ago

#16 - Add fix to ensure VCF evidence is properly picked up for revcomp ins

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

#15 - Cicd docs

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

#14 - gumpy doesn't check that the `REF` field in a vcf file matches what it is the `Genome` object when adding

Issue - State: open - Opened by philipwfowler almost 2 years ago - 1 comment

#13 - Ensure position is recorded for split deletions

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

#12 - Large deletions + VCF Evidence

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

#11 - Minor fixes for minority populations

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

#10 - Added various fixes

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

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

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

#8 - Minor alleles

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

#7 - Fix issue which caused error during VCF parsing

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

#6 - Remove save load

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

#5 - Fix aa issues

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

#4 - Fixed issue with not adding synonymous amino acid mutations to GeneDi…

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

#3 - Added install requirements to setup.cfg to ensure requirements installed

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

#2 - Develop vcf

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

#1 - Develop optimise

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