Ecosyste.ms: Issues

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

GitHub / iqbal-lab/Mykrobe-predictor issues and pull requests

#154 - Index error on version 0.6.1

Issue - State: closed - Opened by cytang19 almost 6 years ago - 3 comments

#153 - Resistance prediction for mixed isolates

Issue - State: closed - Opened by AdmiralenOla almost 6 years ago - 3 comments

#152 - Update README to point to new repo

Pull Request - State: closed - Opened by Phelimb about 6 years ago - 1 comment

#151 - --ont flag gives error message

Issue - State: closed - Opened by cytang19 about 6 years ago - 1 comment

#150 - Coll et al lineage/sub-lineage from Mykrobe

Issue - State: closed - Opened by flashton2003 over 6 years ago - 2 comments

#149 - updated readme with information zam gave to me

Pull Request - State: closed - Opened by flashton2003 over 6 years ago - 3 comments

#148 - Type Error : Write()

Issue - State: closed - Opened by idolawoye over 6 years ago - 4 comments

#147 - Failing to run Phelim/mykrobe_predictor

Issue - State: closed - Opened by kristyhoran over 6 years ago - 4 comments

#146 - Inconsistency between Myrkrobe results and assembly

Issue - State: open - Opened by saschako812 about 7 years ago - 8 comments

#144 - Question about resistance report. R vs r

Issue - State: closed - Opened by harrismia about 7 years ago - 2 comments

#143 - confidence_threshold bug

Issue - State: closed - Opened by Takadonet about 7 years ago - 2 comments

#142 - PyPi releases do not include the license file

Issue - State: open - Opened by mbargull about 7 years ago

#141 - Request: save the .json file for later use

Issue - State: closed - Opened by RaSieb about 7 years ago - 4 comments
Labels: enhancement

#140 - Error with install on linux / python 3.6

Issue - State: closed - Opened by RaSieb about 7 years ago - 2 comments

#139 - __init__() got an unexpected keyword argument 'include_hom_alt_calls'

Issue - State: closed - Opened by daarojasos over 7 years ago - 1 comment

#138 - Add model to output

Pull Request - State: closed - Opened by Phelimb over 7 years ago

#137 - Remove win installer and inno setup

Pull Request - State: closed - Opened by ffranr over 7 years ago

#136 - log messages explicitly sent to stdout

Pull Request - State: closed - Opened by ffranr over 7 years ago

#135 - added instructions and config files for building win64 installer

Pull Request - State: closed - Opened by ffranr over 7 years ago

#134 - Can we get summary for the result

Issue - State: closed - Opened by yujun2017 over 7 years ago - 2 comments

#133 - Fix UI build

Pull Request - State: closed - Opened by simonheys over 7 years ago

#132 - need a option for the output file

Issue - State: closed - Opened by yujun2017 over 7 years ago - 3 comments

#130 - "mccortex geno" invalid command

Issue - State: closed - Opened by RaSieb over 7 years ago - 4 comments

#129 - make compare.py python3 compatible

Pull Request - State: closed - Opened by antunderwood over 7 years ago

#128 - mccortex to latest

Pull Request - State: closed - Opened by Phelimb over 7 years ago

#127 - Added missing species panel to dist

Pull Request - State: closed - Opened by Phelimb over 7 years ago

#126 - IndexError: list index out of range exception on Linux but not Mac

Issue - State: closed - Opened by harrismia over 7 years ago - 9 comments

#125 - mykrobe predictor error

Issue - State: closed - Opened by vsrinivasanoucru over 7 years ago - 2 comments

#124 - Removed tomidae + ratisbonense from TB species probe set

Pull Request - State: closed - Opened by Phelimb almost 8 years ago

#123 - Format of Variants Column

Issue - State: open - Opened by Owen-haha almost 8 years ago - 3 comments

#122 - mykrobe predict: error: argument species:

Issue - State: closed - Opened by hirenbioinfo almost 8 years ago - 3 comments

#121 - Develop

Pull Request - State: closed - Opened by Phelimb almost 8 years ago

#120 - mykrobe errors with: AttributeError: 'Namespace' object has no attribute 'ont'

Issue - State: closed - Opened by antunderwood about 8 years ago - 2 comments

#119 - Probeset Documentation

Issue - State: open - Opened by RaSieb about 8 years ago - 9 comments

#118 - Failing to call high freq R allele, saying log lik R== log lik r

Issue - State: closed - Opened by iqbal-lab about 8 years ago - 2 comments

#117 - Ont issue 116

Pull Request - State: closed - Opened by Phelimb about 8 years ago - 1 comment

#116 - Stop printing r calls for nanopore data

Issue - State: closed - Opened by iqbal-lab about 8 years ago

#115 - Remove requirement of seeing 100% of an allele for nanopore data

Issue - State: closed - Opened by iqbal-lab about 8 years ago - 1 comment

#114 - fix for atlas requirement clash (reported by several users)

Pull Request - State: closed - Opened by Phelimb about 8 years ago

#113 - Json_to_tsv script in Docker

Issue - State: closed - Opened by dankein over 8 years ago - 1 comment

#112 - Using population genome graphs for genotyping

Issue - State: open - Opened by ytliuSVN over 8 years ago - 2 comments

#111 - Ensuring probes do not extend too far

Issue - State: closed - Opened by iqbal-lab over 8 years ago - 1 comment

#110 - Probe generation and paralogs

Issue - State: closed - Opened by iqbal-lab over 8 years ago - 1 comment

#109 - Update documentation and error handling for default skeleton writing

Issue - State: closed - Opened by rrwick over 8 years ago - 3 comments

#108 - Mixtures results are ambiguous without prior knowledge of subspecies

Issue - State: closed - Opened by Phelimb over 8 years ago - 1 comment

#107 - llatzerense species has a bug in reporting u'percent_coverage

Issue - State: closed - Opened by Phelimb over 8 years ago

#106 - paired-end reads

Issue - State: closed - Opened by afkoeppel over 8 years ago - 1 comment

#105 - new release integrating python code into exe for app

Issue - State: closed - Opened by iqbal-lab over 8 years ago - 1 comment

#104 - genotype error

Issue - State: closed - Opened by RaSieb over 8 years ago - 3 comments

#103 - Pulling m2 into master

Issue - State: closed - Opened by Phelimb almost 9 years ago - 1 comment

#102 - Use tmp dir instead of hardcoded /tmp/

Issue - State: closed - Opened by Phelimb almost 9 years ago

#101 - Wrapping install

Issue - State: closed - Opened by iqbal-lab almost 9 years ago

#100 - We could do with a new release, no?

Issue - State: closed - Opened by iqbal-lab about 9 years ago - 2 comments

#99 - We should document how to parallelise

Issue - State: closed - Opened by iqbal-lab about 9 years ago - 1 comment

#98 - Possible floating point error when calculating DFR* thresholds

Issue - State: closed - Opened by Phelimb about 9 years ago - 4 comments

#97 - Windows XP

Issue - State: closed - Opened by milieuziektes about 9 years ago - 4 comments

#96 - seq_file.c:255: Warning -- plain file starts with non-ACGTN

Issue - State: closed - Opened by FelipeMelis about 9 years ago - 8 comments

#95 - Problem with code_generator

Issue - State: closed - Opened by FelipeMelis about 9 years ago - 7 comments

#93 - Makefile:153: recipe for target 'predictor' failed

Issue - State: closed - Opened by tseemann about 9 years ago - 7 comments

#92 - Report missing WT even when an alternate cannot be found

Issue - State: closed - Opened by Phelimb about 9 years ago - 1 comment

#91 - ImportError: cannot import name unique

Issue - State: closed - Opened by tseemann over 9 years ago - 5 comments

#90 - Force resistance predictions if species is not target species.

Pull Request - State: closed - Opened by Phelimb over 9 years ago - 28 comments

#89 - Extending

Pull Request - State: closed - Opened by Phelimb over 9 years ago

#88 - Document special case of Clinda output

Issue - State: closed - Opened by Phelimb over 9 years ago

#87 - allow amplicon data

Issue - State: closed - Opened by stephenturner over 9 years ago - 5 comments

#86 - output documentation & parser

Issue - State: closed - Opened by stephenturner over 9 years ago - 8 comments

#85 - Add version string to JSON output

Issue - State: closed - Opened by Phelimb over 9 years ago

#84 - Memory leaks in test code

Issue - State: closed - Opened by iqbal-lab over 9 years ago - 2 comments

#83 - Unhandled option in switch

Issue - State: closed - Opened by iqbal-lab over 9 years ago - 1 comment

#82 - Linezolid support added but incomplete

Issue - State: closed - Opened by iqbal-lab over 9 years ago - 1 comment

#81 - Use only virulence genes suggested by Claire Gordon

Issue - State: closed - Opened by iqbal-lab over 9 years ago - 1 comment

#80 - Unit tests do not compile on tip of master

Issue - State: closed - Opened by iqbal-lab over 9 years ago

#79 - Code to remove from code-generator

Issue - State: closed - Opened by iqbal-lab over 9 years ago - 5 comments

#78 - Unhandled case in switch

Issue - State: closed - Opened by iqbal-lab over 9 years ago

#77 - Added empirical frequency/CN thresholds to reduce FP

Pull Request - State: closed - Opened by Phelimb over 9 years ago - 1 comment

#76 - Installation Error: 1

Issue - State: closed - Opened by AC-genomics over 9 years ago - 6 comments

#75 - Installation Error 1

Issue - State: closed - Opened by AC-genomics over 9 years ago - 1 comment

#74 - Don't display r if coverage is better explained by a contaminating species than by target species.

Issue - State: closed - Opened by Phelimb over 9 years ago - 5 comments
Labels: enhancement

#73 - Consider adding this diverged mecA to panel

Issue - State: closed - Opened by Phelimb over 9 years ago
Labels: enhancement

#72 - Mtb Streptomycin resistance - Balloux mutation

Issue - State: closed - Opened by iqbal-lab over 9 years ago

#71 - Docker version

Pull Request - State: closed - Opened by mattbates over 9 years ago

#70 - Added free mask where necessary to fix memory leak. #45

Pull Request - State: closed - Opened by Phelimb almost 10 years ago - 5 comments

#61 - Stop printing pyrazinamide results

Issue - State: closed - Opened by iqbal-lab almost 10 years ago - 1 comment
Labels: bug

#59 - Missing checks for malloc failures

Issue - State: closed - Opened by iqbal-lab almost 10 years ago - 4 comments

#58 - Error handling - handle no data

Issue - State: closed - Opened by iqbal-lab almost 10 years ago
Labels: enhancement

#56 - UI issue - better ordering of views/tabs

Issue - State: closed - Opened by iqbal-lab almost 10 years ago
Labels: enhancement

#49 - del

Issue - State: closed - Opened by iqbal-lab almost 10 years ago - 1 comment
Labels: enhancement

#45 - (Trivial) Memory leaks in new species code

Issue - State: closed - Opened by Phelimb almost 10 years ago - 5 comments

#33 - Improve species id

Issue - State: closed - Opened by iqbal-lab about 10 years ago - 1 comment
Labels: enhancement

#32 - Add Oryx Africanum A and B to panel

Issue - State: closed - Opened by Phelimb about 10 years ago - 3 comments
Labels: enhancement

#28 - Bad call on C00001215

Issue - State: closed - Opened by Phelimb about 10 years ago - 7 comments
Labels: bug

#27 - Update staph panel using Michel's info

Issue - State: closed - Opened by iqbal-lab about 10 years ago - 6 comments

#26 - Automated means of extending gene panel with a training set

Issue - State: closed - Opened by iqbal-lab about 10 years ago - 1 comment

#25 - del

Issue - State: closed - Opened by iqbal-lab about 10 years ago
Labels: enhancement

#24 - Make susceptibility calls based on median coverage in mixed.

Issue - State: closed - Opened by Phelimb over 10 years ago - 3 comments
Labels: enhancement

#16 - No evidence given for inducible Clindamycin resistance

Issue - State: closed - Opened by iqbal-lab over 10 years ago - 3 comments

#15 - Add cmd_line option to output start and end times in JSON

Issue - State: closed - Opened by Phelimb over 10 years ago
Labels: enhancement