nextstrain/augur issues and pull requests

#874 - Fix/parse fix dates

Pull Request - State: closed - Opened by rneher almost 3 years ago - 5 comments

#867 - dataset schema (v2) is out of date

Issue - State: closed - Opened by jameshadfield almost 3 years ago - 1 comment

#866 - Support databases

Issue - State: open - Opened by victorlin almost 3 years ago - 6 comments
Labels: enhancement

#864 - Validate root-sequence output

Issue - State: open - Opened by jameshadfield almost 3 years ago - 1 comment
Labels: enhancement

#863 - Running tests adds untracked files

Issue - State: closed - Opened by jameshadfield almost 3 years ago - 3 comments
Labels: bug

#860 - Add `augur curate` subcommands

Issue - State: closed - Opened by huddlej almost 3 years ago - 26 comments
Labels: enhancement

#857 - Move Uppercase after camelCase in parse.prettify

Pull Request - State: open - Opened by emmahodcroft almost 3 years ago - 2 comments

#857 - Move Uppercase after camelCase in parse.prettify

Pull Request - State: open - Opened by emmahodcroft almost 3 years ago - 2 comments

#856 - UFBoot values are parsed incorrectly by refine and interfere with ancestral resulting in odd annotations

Issue - State: open - Opened by ammaraziz almost 3 years ago - 4 comments
Labels: bug, needs triage

#854 - filter: re-implement with SQLite and add option to use with `--engine`

Pull Request - State: closed - Opened by victorlin almost 3 years ago - 15 comments

#829 - io: Pass encoding and newline keyword arguments to `open_file`

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

#824 - Add notebook for parsing json to ete tree objects for downstream analysis

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

#820 - Can the software do phylogenetic trees based on protein multiple sequence alignment data

Issue - State: closed - Opened by tanxiaoqin888 about 3 years ago - 1 comment
Labels: documentation

#817 - Unclear which version is referred to by `stable`: add `stable` version number visibly

Issue - State: closed - Opened by corneliusroemer about 3 years ago - 2 comments
Labels: low priority, documentation

#814 - Provide notebook or script to parse exported JSON into a tree object for downstream analysis

Issue - State: closed - Opened by sidneymbell about 3 years ago - 2 comments
Labels: documentation

#812 - io: Parse metadata with C engine, restrict to either CSV or TSV

Pull Request - State: closed - Opened by victorlin about 3 years ago - 7 comments

#811 - Augur Traits - Problems with assigning concrete traits

Issue - State: closed - Opened by MichaelP93 about 3 years ago - 8 comments
Labels: bug

#811 - Augur Traits - Problems with assigning concrete traits

Issue - State: closed - Opened by MichaelP93 about 3 years ago - 8 comments
Labels: bug

#810 - read_metadata: Allow graceful handling of duplicate strain names

Issue - State: closed - Opened by corneliusroemer about 3 years ago - 5 comments
Labels: enhancement

#809 - filter: Rewrite priority queue logic with pandas functions

Pull Request - State: closed - Opened by victorlin about 3 years ago - 4 comments

#805 - Implement subsampling as a script (or eventually "augur subsample")

Issue - State: closed - Opened by DSequ about 3 years ago - 3 comments
Labels: duplicate, Epic

#789 - Speed up filtering by not processing entire file

Issue - State: closed - Opened by trvrb about 3 years ago - 30 comments
Labels: enhancement

#769 - [augur tree] input alignment must end in .fasta

Issue - State: closed - Opened by jameshadfield over 3 years ago - 7 comments
Labels: bug, easy problem

#764 - augur translate: ValueError("No records found in handle")

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

#764 - augur translate: ValueError("No records found in handle")

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

#753 - Remove Snakemake as a dependency

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

#749 - Apply filters in a loop

Pull Request - State: closed - Opened by huddlej over 3 years ago - 2 comments

#740 - filter: Support relative dates for `--min-date` and `--max-date`

Pull Request - State: closed - Opened by benjaminotter over 3 years ago - 23 comments
Labels: enhancement, moderate priority, easy problem

#734 - Divergence (mutations) on the root node are ignored by augur export

Issue - State: open - Opened by jameshadfield over 3 years ago
Labels: bug, easy problem

#731 - io: Do not use multiple threads to write compressed files

Issue - State: open - Opened by huddlej over 3 years ago - 1 comment
Labels: bug

#728 - Allow users to specify arbitrary branch & clade labels

Pull Request - State: closed - Opened by jameshadfield over 3 years ago - 15 comments

#726 - Support compression presets for LZMA compression backend

Issue - State: open - Opened by huddlej over 3 years ago - 6 comments
Labels: enhancement

#726 - Support compression presets for LZMA compression backend

Issue - State: open - Opened by huddlej over 3 years ago - 6 comments
Labels: enhancement

#725 - read_metadata: Provide an interface to resolve duplicate strain names in metadata

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

#720 - Ability to export branch labels

Issue - State: closed - Opened by jameshadfield almost 4 years ago - 1 comment

#719 - augur export produces duplicate colorings

Issue - State: closed - Opened by jameshadfield almost 4 years ago
Labels: bug

#697 - WIP: Support multiple inputs during filter

Pull Request - State: open - Opened by huddlej almost 4 years ago

#696 - Support compressed alignments

Pull Request - State: open - Opened by huddlej almost 4 years ago - 3 comments

#667 - augur tools do not recognize purely numeric strain IDs

Issue - State: closed - Opened by dpark01 about 4 years ago - 5 comments
Labels: bug, moderate priority

#642 - Catch exceptions in the command line interface and print error messages to stderr

Issue - State: closed - Opened by huddlej about 4 years ago - 4 comments
Labels: bug, priority: high, moderate problem

#635 - augur subsample command

Issue - State: open - Opened by jameshadfield about 4 years ago - 4 comments
Labels: enhancement

#634 - Add warning to docs fetched by docs.nextstrain.org

Pull Request - State: closed - Opened by eharkins about 4 years ago - 2 comments

#614 - RFC: separating CLI and library code

Pull Request - State: closed - Opened by elebow over 4 years ago - 2 comments

#614 - RFC: separating CLI and library code

Pull Request - State: closed - Opened by elebow over 4 years ago - 2 comments

#606 - Refactor JSON Schema validation into new classes

Pull Request - State: closed - Opened by elebow over 4 years ago - 2 comments

#606 - Refactor JSON Schema validation into new classes

Pull Request - State: closed - Opened by elebow over 4 years ago - 2 comments

#603 - Fix flake errors

Pull Request - State: closed - Opened by huddlej over 4 years ago - 5 comments

#591 - Error in translate.py from vcf

Issue - State: closed - Opened by andreott over 4 years ago - 3 comments
Labels: bug, high priority, easy problem

#586 - Provide options to handle duplicate sequences more gracefully in augur filter

Issue - State: closed - Opened by huddlej over 4 years ago - 1 comment
Labels: enhancement, needs triage

#583 - Understand mutations produced by augur

Issue - State: closed - Opened by biocyberman over 4 years ago - 6 comments
Labels: documentation, faq

#583 - Understand mutations produced by augur

Issue - State: closed - Opened by biocyberman over 4 years ago - 6 comments
Labels: documentation, faq

#557 - Make snakemake a dev dependency

Pull Request - State: closed - Opened by huddlej over 4 years ago - 9 comments

#549 - Execute Cram via pytest

Pull Request - State: closed - Opened by vanguard737 over 4 years ago - 2 comments

#549 - Execute Cram via pytest

Pull Request - State: closed - Opened by vanguard737 over 4 years ago - 2 comments

#543 - [RFC] Functional tests with Cram

Pull Request - State: closed - Opened by vanguard737 almost 5 years ago - 8 comments

#543 - [RFC] Functional tests with Cram

Pull Request - State: closed - Opened by vanguard737 almost 5 years ago - 8 comments

#540 - Adding a full example to the tests data directory

Issue - State: closed - Opened by Zsailer almost 5 years ago - 5 comments
Labels: enhancement

#540 - Adding a full example to the tests data directory

Issue - State: closed - Opened by Zsailer almost 5 years ago - 5 comments
Labels: enhancement

#535 - Example of integration test using pytest

Pull Request - State: closed - Opened by jameshadfield almost 5 years ago - 2 comments

#525 - WIP/RFC: Add tests for ancestral.py

Pull Request - State: closed - Opened by vanguard737 almost 5 years ago - 6 comments

#525 - WIP/RFC: Add tests for ancestral.py

Pull Request - State: closed - Opened by vanguard737 almost 5 years ago - 6 comments

#522 - Get path and list of mutations between to strains?

Issue - State: closed - Opened by biocyberman almost 5 years ago - 3 comments
Labels: documentation

#522 - Get path and list of mutations between to strains?

Issue - State: closed - Opened by biocyberman almost 5 years ago - 3 comments
Labels: documentation

#509 - [WIP] CLI and init improvements

Pull Request - State: closed - Opened by groutr almost 5 years ago - 5 comments

#507 - [BUG] augur mask only supports VCFs with a single "chromosome" entry

Issue - State: open - Opened by huddlej almost 5 years ago - 8 comments
Labels: bug, low priority, moderate problem

#505 - [Feature request] GPU acceleration?

Issue - State: closed - Opened by calebwin almost 5 years ago - 3 comments
Labels: enhancement

#505 - [Feature request] GPU acceleration?

Issue - State: closed - Opened by calebwin almost 5 years ago - 3 comments
Labels: enhancement

#504 - [WIP] add initial tests for reconstruct_sequences.py

Pull Request - State: closed - Opened by Zsailer almost 5 years ago - 1 comment

#504 - [WIP] add initial tests for reconstruct_sequences.py

Pull Request - State: closed - Opened by Zsailer almost 5 years ago - 1 comment

#497 - [BUG] AttributeError can be thrown by the run function in augur/traits.py

Issue - State: closed - Opened by terrycojones almost 5 years ago - 1 comment
Labels: bug

#497 - [BUG] AttributeError can be thrown by the run function in augur/traits.py

Issue - State: closed - Opened by terrycojones almost 5 years ago - 1 comment
Labels: bug

#494 - WIP and RFC: Rewrite `filter.py` with several classes

Pull Request - State: closed - Opened by elebow almost 5 years ago - 15 comments

#494 - WIP and RFC: Rewrite `filter.py` with several classes

Pull Request - State: closed - Opened by elebow almost 5 years ago - 15 comments

#492 - [WIP] Add tests for clades and add black code format

Pull Request - State: closed - Opened by willingc almost 5 years ago - 3 comments

#492 - [WIP] Add tests for clades and add black code format

Pull Request - State: closed - Opened by willingc almost 5 years ago - 3 comments

#489 - [BUG] nt_muts.json might miss some variants?

Issue - State: closed - Opened by mgalardini almost 5 years ago - 3 comments
Labels: bug, needs triage

#489 - [BUG] nt_muts.json might miss some variants?

Issue - State: closed - Opened by mgalardini almost 5 years ago - 3 comments
Labels: bug, needs triage

#473 - Update the conda channels list in environment.yml

Issue - State: closed - Opened by willingc almost 5 years ago - 1 comment
Labels: enhancement

#473 - Update the conda channels list in environment.yml

Issue - State: closed - Opened by willingc almost 5 years ago - 1 comment
Labels: enhancement

#472 - Improve startup time

Issue - State: open - Opened by willingc almost 5 years ago - 19 comments
Labels: enhancement

#464 - Want to contribute? Welcome! Please start here.

Issue - State: closed - Opened by sidneymbell almost 5 years ago - 4 comments

#464 - Want to contribute? Welcome! Please start here.

Issue - State: closed - Opened by sidneymbell almost 5 years ago - 4 comments

#438 - Feature request: Command to convert .json to .nwk

Issue - State: closed - Opened by mvolz about 5 years ago - 9 comments
Labels: enhancement, priority: low

#438 - Feature request: Command to convert .json to .nwk

Issue - State: closed - Opened by mvolz about 5 years ago - 9 comments
Labels: enhancement, priority: low

#421 - Source canonical Nextstrain environment file for Travis CI

Pull Request - State: closed - Opened by trvrb about 5 years ago - 12 comments
Labels: moderate priority, easy problem

#391 - Warn if `export v1` Using a v5 Translate File

Pull Request - State: closed - Opened by emmahodcroft over 5 years ago - 3 comments
Labels: v6

#352 - ancestral reconstruction for `N` nts should be opt in

Issue - State: closed - Opened by jameshadfield over 5 years ago - 7 comments
Labels: needs triage

#342 - Allow "?" for URL attributes in schema

Pull Request - State: closed - Opened by trvrb over 5 years ago - 3 comments

#313 - improve format of help messages

Issue - State: open - Opened by jameshadfield over 5 years ago - 3 comments
Labels: bug

#273 - Allow "minimal" augur export

Issue - State: closed - Opened by trvrb almost 6 years ago - 5 comments
Labels: enhancement, moderate priority, moderate problem, office-hours

#264 - allow working straight of an amino acid alignment

Pull Request - State: closed - Opened by rneher almost 6 years ago

#242 - Create a guide for contributing code to augur

Issue - State: closed - Opened by huddlej about 6 years ago - 5 comments
Labels: enhancement, documentation

#242 - Create a guide for contributing code to augur

Issue - State: closed - Opened by huddlej about 6 years ago - 5 comments
Labels: enhancement, documentation

#125 - Censor tip frequencies and titer measurements

Pull Request - State: closed - Opened by huddlej over 6 years ago

#123 - DRM Mapping Working for TB

Pull Request - State: closed - Opened by emmahodcroft over 6 years ago

#108 - H1N1pdm failing due to mismatched epitope mask length

Issue - State: closed - Opened by trvrb almost 7 years ago - 5 comments

#35 - Store titer records in TiterRecord class and export in structured JSON format

Issue - State: open - Opened by huddlej over 7 years ago - 2 comments
Labels: enhancement, priority: low, easy problem

#35 - Store titer records in TiterRecord class and export in structured JSON format

Issue - State: open - Opened by huddlej over 7 years ago - 1 comment
Labels: enhancement, priority: low, easy problem

GitHub / nextstrain/augur issues and pull requests