Ecosyste.ms: Issues

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

GitHub / cov-lineages/scorpio issues and pull requests

#51 - Dev

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

#50 - Tidy and add tests

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

#48 - Pangolin v1.12 as used by GISAID misclassifies a lot of true BA.5* as BA.2*

Issue - State: open - Opened by corneliusroemer over 2 years ago - 2 comments
Labels: scorpio

#47 - Scorpio: Many BA.4/5 misclassified as BA.2* because "Probable Omicron (BA.2-like)"

Issue - State: open - Opened by corneliusroemer over 2 years ago - 26 comments
Labels: scorpio

#46 - hundred XM genomes called as 'Unassigned' or as BA.1

Issue - State: closed - Opened by akifoss over 2 years ago - 5 comments
Labels: scorpio, pangoLEARN

#45 - Scorpio overriding UShER calls for XD recombinants

Issue - State: open - Opened by SVN-PhD over 2 years ago - 1 comment
Labels: scorpio

#44 - handle recombinant assignments that dont pass both parents- dont acce…

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

#43 - Dev

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

#42 - Handle multiple levels of definition within a constellation

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

#41 - Giving input file without `-i` causes stack trace

Issue - State: closed - Opened by rambaut about 3 years ago
Labels: enhancement

#40 - Add check that scorpio file is compatible with current scorpio version

Issue - State: open - Opened by rambaut about 3 years ago
Labels: enhancement

#39 - add option to skip translation to aa

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

#38 - Dev

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

#37 - Make scorpio multithreaded

Issue - State: closed - Opened by rmcolq about 3 years ago
Labels: enhancement

#36 - Allow mutation strings to have comments at the end (if this doesn't work already)

Issue - State: closed - Opened by rambaut about 3 years ago - 1 comment
Labels: enhancement

#34 - small bug fixes

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

#33 - fastq as input data

Issue - State: closed - Opened by carlottaolivero about 3 years ago - 1 comment

#32 - scorpio overriding AY.4.2 to B.1.617.2 on very few Ns

Issue - State: closed - Opened by mcroxen about 3 years ago - 12 comments

#31 - Dev

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

#30 - Enable multiple constellation files for the same "constellation"

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

#29 - Allow for a rule with more flexibility for indels

Issue - State: closed - Opened by rmcolq over 3 years ago - 2 comments

#28 - Fix bugs with define

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

#27 - Dev

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

#26 - Do a 'union' haplotype of multiple definition files.

Issue - State: closed - Opened by rambaut over 3 years ago - 1 comment
Labels: enhancement

#25 - For `haplotype` command only use one directory of constellation files.

Issue - State: closed - Opened by rambaut over 3 years ago - 2 comments
Labels: enhancement

#24 - Dev

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

#23 - Dev

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

#21 - Scorpio version reporting 0.3.5 incorrectly (?)

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

#20 - merge in dev

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

#19 - Dev

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

#18 - Mutation information

Issue - State: closed - Opened by santoshe1 over 3 years ago - 2 comments

#17 - Dev

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

#16 - Dev

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

#15 - Bug in scorpio

Issue - State: closed - Opened by animesh-workplace over 3 years ago - 9 comments

#14 - Merge in dev

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

#13 - Improve deletion handling

Issue - State: closed - Opened by rmcolq over 3 years ago

#12 - Handle changed constellation labels

Issue - State: closed - Opened by rmcolq over 3 years ago

#10 - Create an optional interspersion statistic

Issue - State: open - Opened by rmcolq over 3 years ago

#8 - CDS orf1a at position 741 is L, but reference sequence has F

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

#7 - Enable protein based mutation definitions e.g. NSP1

Issue - State: closed - Opened by rmcolq over 3 years ago

#5 - Add command line args for intermediate thresholds for `define`

Issue - State: closed - Opened by rmcolq over 3 years ago

#4 - In `define` output intermediates in nice format

Issue - State: closed - Opened by rmcolq over 3 years ago

#3 - Allow outgroups to be specified when running `define`

Issue - State: closed - Opened by rmcolq over 3 years ago

#1 - Add support score when haplotyping/classifying

Issue - State: closed - Opened by rmcolq over 3 years ago