phac-nml/biohansel issues and pull requests

#146 - Patch release v2.6.1

Pull Request - State: closed - Opened by peterk87 over 3 years ago

#145 - Patch fix for Bioconda

Pull Request - State: closed - Opened by peterk87 over 3 years ago

#144 - Release v2.6.0

Pull Request - State: closed - Opened by peterk87 over 3 years ago

#143 - Release v2.6.0

Pull Request - State: closed - Opened by peterk87 over 3 years ago

#142 - Purpose of max kmer frequency?

Issue - State: open - Opened by peterk87 over 3 years ago - 5 comments

#141 - Add bump2version config for easy version updating

Pull Request - State: closed - Opened by peterk87 over 3 years ago

#140 - Covid19

Pull Request - State: closed - Opened by jrober84 over 3 years ago - 1 comment

#139 - Update pypi_deploy.yml

Pull Request - State: closed - Opened by peterk87 almost 4 years ago

#138 - Sync master with the development branch as releases were done from this branch

Pull Request - State: closed - Opened by kbessonov1984 almost 4 years ago

#137 - Github Action for CI

Pull Request - State: closed - Opened by peterk87 almost 4 years ago

#136 - PyPI deploy action

Pull Request - State: closed - Opened by peterk87 almost 4 years ago

#135 - Display warning to user when k-mer length is below specific threshold

Issue - State: open - Opened by glabbe almost 4 years ago
Labels: qc

#134 - Decouple schemes from codebase and put in separate schemes repo

Issue - State: open - Opened by glabbe almost 4 years ago
Labels: enhancement

#133 - Need to add scheme and scheme version to tech results output

Issue - State: open - Opened by glabbe almost 4 years ago
Labels: qc

#132 - Readthedocs

Pull Request - State: closed - Opened by glabbe about 4 years ago - 1 comment

#131 - Update to S. Typhi scheme and metadata

Pull Request - State: closed - Opened by glabbe about 4 years ago
Labels: enhancement

#130 - Update const.py

Pull Request - State: closed - Opened by glabbe about 4 years ago

#129 - Update to S. Typhi scheme and metadata

Pull Request - State: closed - Opened by glabbe about 4 years ago
Labels: enhancement

#128 - Update needed for S. Typhi scheme

Issue - State: closed - Opened by glabbe about 4 years ago - 2 comments
Labels: enhancement, in progress

#127 - Glabbe patch 1 1

Pull Request - State: closed - Opened by glabbe about 4 years ago

#126 - IRIDA-Biohansel: Adding our own schema for other Species

Issue - State: open - Opened by ajkarloss about 4 years ago - 3 comments

#125 - Feature Add: Toggle to run all schemes on a sample and report best matching scheme

Issue - State: open - Opened by jrober84 over 4 years ago
Labels: enhancement

#124 - Update author list according to manuscript

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

#123 - Update author list according to manuscript

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

#122 - Updating QC message from "unconfident" to "inconclusive"

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

#121 - Release v2.4.0

Pull Request - State: closed - Opened by peterk87 about 5 years ago - 5 comments

#120 - Fix metadata NA value issue

Pull Request - State: closed - Opened by peterk87 about 5 years ago

#119 - Prepare release v2.4.0

Pull Request - State: closed - Opened by peterk87 about 5 years ago - 2 comments

#118 - Faster reverse complement using translation table

Pull Request - State: closed - Opened by peterk87 about 5 years ago - 1 comment

#117 - Fix author list in README

Pull Request - State: closed - Opened by peterk87 about 5 years ago - 1 comment

#116 - Add #N/A in subtype field of results when no subtype is found

Pull Request - State: closed - Opened by glabbe about 5 years ago - 3 comments

#115 - Adds #N/A in subtype field of results when no subtype is found

Pull Request - State: closed - Opened by glabbe about 5 years ago - 5 comments

#114 - Update default coverage values and clarify help statement

Pull Request - State: closed - Opened by glabbe about 5 years ago

#113 - Output 'NA' as subtype when no subtype found

Pull Request - State: closed - Opened by glabbe about 5 years ago - 2 comments

#112 - Output "NA" as subtype for samples that fail QC with no subtype result or no targets found

Issue - State: closed - Opened by glabbe about 5 years ago - 11 comments

#111 - Readme Update

Pull Request - State: closed - Opened by DarianHole about 5 years ago

#110 - Rename tb_speciation to tb_lineage

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#109 - Fix to include metadata when installing with pip/conda

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

#108 - metadata file type

Issue - State: closed - Opened by dankein over 5 years ago - 4 comments

#107 - Change tb_speciation to tb_lineage?

Issue - State: closed - Opened by dankein over 5 years ago - 4 comments

#106 - Fix deployment to PyPI

Pull Request - State: closed - Opened by peterk87 over 5 years ago

#105 - Try fix #104 deploy.on.repo travis ci

Pull Request - State: closed - Opened by peterk87 over 5 years ago

#104 - Skipping a deployment with the pypi provider because this repo's name does not match one specified in .travis.yml's deploy.on.repo: phac-nml/bio_hansel

Issue - State: closed - Opened by peterk87 over 5 years ago

#103 - Update to TB_Speciation and Typhi subtyping schemes

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#102 - Update schemes for tb_speciation and typhi, including metadata

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

#101 - Raise MAX_KMER_FREQUENCY Value to 10,000

Issue - State: closed - Opened by glabbe over 5 years ago - 1 comment

#100 - Fix #98 QC check for mixed subtypes

Pull Request - State: closed - Opened by peterk87 over 5 years ago - 2 comments

#99 - Semicolons in version numbers for some schemes

Issue - State: closed - Opened by peterk87 over 5 years ago - 1 comment

#98 - QC module not failing samples where positive and negative kmers are detected for the same genome position

Issue - State: closed - Opened by glabbe over 5 years ago - 1 comment

#97 - Deploy to PyPI on release

Pull Request - State: closed - Opened by Takadonet over 5 years ago

#96 - Deploy to PyPI on release

Pull Request - State: closed - Opened by peterk87 over 5 years ago

#95 - Update New Release to Pypi

Issue - State: closed - Opened by DarianHole over 5 years ago - 1 comment

#94 - Major upgrade

Pull Request - State: closed - Opened by Takadonet over 5 years ago

#93 - version and author update

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#92 - update enteritidis scheme and typhimurium scheme added

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#91 - Degenerate Base Expansion addition

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

#90 - Fix to issue 88 with new QC Check

Pull Request - State: closed - Opened by DarianHole over 5 years ago - 7 comments

#89 - update enteritidis scheme

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#88 - Not failing QC with inconsistent results in first hierarchical level

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

#87 - small dev bugfix

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#86 - New Schemes Ready

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

#85 - Allow levels past 9

Pull Request - State: closed - Opened by DarianHole over 5 years ago - 6 comments

#84 - Create release on merge to master and deploy to PyPI

Issue - State: closed - Opened by peterk87 over 5 years ago

#83 - Create azure-pipelines.yml

Pull Request - State: closed - Opened by peterk87 over 5 years ago - 3 comments

#82 - Changed 'tile' to 'kmer' to create consistency

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#81 - if no subtype output '#N/A'

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#80 - Update README.rst

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#79 - Revert "NA subtype default output"

Pull Request - State: closed - Opened by peterk87 over 5 years ago

#78 - NA subtype default output

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#77 - Match results orders tiles as positive first

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#76 - Sort tiles

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#75 - Readthedocs

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#74 - Readthedocs

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#73 - Readme update

Pull Request - State: closed - Opened by DarianHole over 5 years ago

#72 - Re-order the match results to put the positive tiles matches at the top of the list

Issue - State: closed - Opened by glabbe over 5 years ago - 1 comment

#71 - fixing fasta lower case no result bug. added a unit test for subtype_contigs function

Pull Request - State: closed - Opened by kbessonov1984 almost 6 years ago

#70 - toupper case bug fix in inputs

Pull Request - State: closed - Opened by kbessonov1984 almost 6 years ago - 2 comments

#69 - When no subtype results, report "NA" in subtype field

Issue - State: closed - Opened by peterk87 almost 6 years ago - 2 comments

#68 - Long form reporting of multiple subtypes for a sample

Issue - State: open - Opened by peterk87 almost 6 years ago
Labels: enhancement

#67 - Collapse mixed subtype results to highest resolution discordant subtypes

Issue - State: open - Opened by peterk87 almost 6 years ago
Labels: enhancement

#66 - Bionumerics CSV output option

Issue - State: closed - Opened by peterk87 almost 6 years ago - 1 comment

#65 - v2.1.1 - Fix command-line parameter and lower-case seq issues

Pull Request - State: closed - Opened by peterk87 almost 6 years ago - 3 comments

#64 - Readthedocs

Pull Request - State: closed - Opened by glabbe almost 6 years ago - 1 comment

#63 - Command-line arg variable name and SubtypingParams instance variable name synchronization

Issue - State: open - Opened by peterk87 almost 6 years ago - 1 comment

#62 - Update utils.py

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

#61 - --min-kmer-freq is no longer adjustable

Issue - State: closed - Opened by sond468 almost 6 years ago

#60 - Degenerate "probe" sequence expansion

Issue - State: closed - Opened by peterk87 almost 6 years ago - 8 comments
Labels: enhancement

#59 - Output list of tiles that didn't match

Issue - State: open - Opened by dankein about 6 years ago - 4 comments
Labels: enhancement

#58 - Scheme creation/tree visualization

Pull Request - State: closed - Opened by gcttong over 6 years ago - 1 comment

#57 - Scheme creation/new changes

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

#55 - Scheme creation/tests

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

#54 - Scheme creation/initial

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

#52 - Scheme creation

Pull Request - State: open - Opened by peterk87 over 6 years ago - 1 comment

#51 - Fix empty output files when no targets are found in inputs

Pull Request - State: closed - Opened by peterk87 over 6 years ago - 1 comment

#50 - Link to docs in readme

Issue - State: closed - Opened by peterk87 over 6 years ago - 1 comment

#47 - Shorten QC messages

Pull Request - State: closed - Opened by peterk87 over 6 years ago - 2 comments

#43 - SNV subtyping scheme creation tool

Issue - State: closed - Opened by gcttong over 6 years ago - 2 comments

#40 - Fix issue #39 - `zcat < file`

Pull Request - State: closed - Opened by peterk87 over 6 years ago

#38 - Add sample input grouping based on the regex `_(R1|R2)` to support Illumina instrument output

Issue - State: closed - Opened by peterk87 over 6 years ago - 1 comment

#23 - Add Aho-Corasick run mode for faster subtyping

Pull Request - State: closed - Opened by peterk87 almost 7 years ago

GitHub / phac-nml/biohansel issues and pull requests