Ecosyste.ms: Issues

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

GitHub / harrispopgen/mutyper issues and pull requests

#50 - New GATK missing genotype annotation

Issue - State: open - Opened by WSDeWitt 5 months ago

#49 - JOSS citation

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

#48 - JOSS requested affiliation edits

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

#47 - JOSS review

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

#46 - Example usage: reduce assumptions

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

#45 - Add State of the field

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

#44 - Add Community Guidelines

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

#43 - Fix Documentation link

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

#41 - Integration with Hail

Issue - State: open - Opened by vladsavelyev over 1 year ago - 1 comment
Labels: enhancement

#40 - JOSS prereview

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

#39 - JOSS paper

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

#38 - numpy implementation for spectra

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

#37 - issue 36: dealing with missing genotypes with mutyper variants

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

#36 - mutyper variants converts missing genotypes to 0

Issue - State: closed - Opened by Lukez-pi over 1 year ago

#35 - Changed the 'number' type of 'mutation type' to A in the VCF header

Pull Request - State: closed - Opened by Lukez-pi about 2 years ago - 3 comments

#34 - Don't count `phase==True` toward genotypes

Pull Request - State: closed - Opened by WSDeWitt about 2 years ago

#33 - CLI tests

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

#31 - Added a fix for adding too many counts when the GT is unknown

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

#30 - more mutyper counts in spectra than expected

Issue - State: closed - Opened by mrvollger over 2 years ago - 13 comments

#29 - Docstweaks

Pull Request - State: closed - Opened by WSDeWitt almost 3 years ago

#28 - Fix for ancestral subcommand compressed fasta input, extra logging info, and a snakemake

Pull Request - State: closed - Opened by mrvollger almost 3 years ago - 1 comment

#27 - Issue with directionality of the chain file and possible fasta indexing bug.

Issue - State: closed - Opened by mrvollger almost 3 years ago - 3 comments

#26 - mutyper targets can't handle compressed bed files

Issue - State: open - Opened by ab08028 about 3 years ago

#25 - 14 strandedness test

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

#24 - Proposed fix to bug #14

Pull Request - State: closed - Opened by RenzoTale88 about 3 years ago

#23 - Fix bug #20

Pull Request - State: closed - Opened by RenzoTale88 about 3 years ago - 1 comment

#22 - spectra for haploids

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

#21 - haploid counting in mutyper spectra

Issue - State: closed - Opened by ab08028 about 3 years ago - 6 comments

#20 - Problem with ancestor command

Issue - State: closed - Opened by RenzoTale88 over 3 years ago - 6 comments

#19 - haploid VCF parsing

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

#18 - polarize genotypes, closes #17

Pull Request - State: closed - Opened by WSDeWitt over 3 years ago - 1 comment

#17 - ancestral polarization of individual genotypes

Issue - State: closed - Opened by WSDeWitt over 3 years ago
Labels: bug

#16 - Randomize feature for spectra

Pull Request - State: closed - Opened by goldmich over 3 years ago - 1 comment

#15 - kSFS

Issue - State: closed - Opened by barlavi1 over 3 years ago - 1 comment

#14 - Strandedness issue

Issue - State: closed - Opened by RenzoTale88 over 3 years ago - 5 comments

#13 - 4 chains parse

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

#11 - performance issues with accessing bgzipped ancestral fastas

Issue - State: open - Opened by WSDeWitt almost 4 years ago - 3 comments

#10 - Population spectra

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

#9 - strand-aware mutation contexts

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

#8 - population mutation spectra?

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

#7 - might need to include the gcc package dependency in setup.py

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

#6 - use strand_file BED argument to orient context instead of collapsing by revcomp

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

#5 - spectra methods for Python API (not just CLI)

Issue - State: open - Opened by WSDeWitt about 4 years ago

#4 - ancestral genome estimation

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

#3 - Create LICENSE

Pull Request - State: closed - Opened by WSDeWitt over 4 years ago

#2 - packagify

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

#1 - docs

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