phac-nml/ecoli_serotyping issues and pull requests

#93 - Ectyper outputs different results depending on input format

Issue - State: closed - Opened by arshdeep1k 4 months ago - 1 comment

#92 - Mismatch in parameters, help text and manuscript

Issue - State: closed - Opened by schorlton 9 months ago - 2 comments

#91 - Sequence not shown. --sequence flag is depricated

Issue - State: closed - Opened by J-JEMINA about 1 year ago - 4 comments

#90 - TODO: Make tool compatible with metadata or mixed reads datasets

Issue - State: open - Opened by kbessonov1984 about 1 year ago
Labels: enhancement

#89 - -o argument is required

Issue - State: closed - Opened by mediator01 over 1 year ago - 2 comments
Labels: bug

#87 - Unable to identiify species, even in the representative genome of E.coli

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

#86 - New Feature: support for reads compressed in gzip and bzip2 format

Pull Request - State: closed - Opened by crashfrog over 2 years ago - 8 comments

#85 - TODO: Add O-antigen subtype information to the output

Issue - State: open - Opened by kbessonov1984 almost 3 years ago
Labels: enhancement

#84 - Refseq currency check ignores the -r (--refseq) argument

Issue - State: closed - Opened by fda-rapid-cfsan-rge over 3 years ago - 2 comments

#83 - Improve species identification reliability on edge cases or poor quality inputs

Issue - State: open - Opened by kbessonov1984 about 4 years ago

#82 - Version 1.0.0 release

Pull Request - State: closed - Opened by kbessonov1984 over 4 years ago
Labels: enhancement

#81 - Can you please explain the QC?

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

#80 - Switch off E.coli serotype prediction for E.albertii stains

Issue - State: closed - Opened by kbessonov1984 almost 5 years ago - 1 comment

#79 - Failed lookup of assembly GCF_000092525

Issue - State: closed - Opened by Takadonet almost 5 years ago - 2 comments

#78 - Version 0.9.1 addressing minor issues on species identification and fasta files handling

Pull Request - State: closed - Opened by kbessonov1984 almost 5 years ago - 2 comments

#77 - Run getting halted in between with error code b

Issue - State: closed - Opened by aryasuresh234 almost 5 years ago - 4 comments

#76 - Genome name not extracted from filepath

Issue - State: closed - Opened by JanMoat almost 5 years ago - 3 comments

#75 - Paired-end reads

Issue - State: closed - Opened by simone-pignotti about 5 years ago - 3 comments

#74 - ecTyper version 0.9.0 with improved reporting and O-antigen call rate

Pull Request - State: closed - Opened by kbessonov1984 about 5 years ago - 1 comment

#73 - Updated README and meta file for Bioconda to be v0.8.1

Pull Request - State: closed - Opened by chadlaing about 6 years ago

#72 - Galaxy

Pull Request - State: closed - Opened by chadlaing about 6 years ago

#71 - Version bump

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

#70 - version bump

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

#69 - Prediction update

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

#68 - version bump

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

#67 - All temp

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

#66 - Added option to specify temporary directory root. The actual temp dir…

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

#65 - New alleles

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

#64 - Intermediate files for fastq -> fasta now named after the file, rathe…

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

#63 - Multicore

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

#62 - Multicore

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

#61 - MERGE: report raw alignment.title

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

#60 - Multicore

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

#59 - Allele

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

#58 - Standalone VF Tool

Issue - State: open - Opened by kevinkle over 6 years ago
Labels: wontfix, good beginner task

#57 - Allele

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

#56 - Allele

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

#55 - Allele

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

#54 - ectyper -h should report version information

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

#53 - Use importlib.resources for files in ectyper/Data/

Issue - State: open - Opened by kevinkle over 6 years ago

#52 - ADD: cross-compatibility with either Python2 or Python3

Pull Request - State: open - Opened by kevinkle almost 7 years ago - 5 comments

#51 - ADD: travis badge

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

#50 - ADD: travis badge

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

#49 - Updated wording of the README.

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

#48 - Merged branch with all of Sam and Rylan's changes

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

#47 - Galaxy

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

#46 - add anaconda to required channels in README

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

#45 - Added changes to fix some usability issue inspired by galaxy deployment

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

#44 - fixed issue where duplicate alleles from EcOH were removed

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

#43 - Added option to bypass ecoli verification

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

#42 - remove benchmark data

Pull Request - State: closed - Opened by dev-ansung about 7 years ago

#41 - Tweak chunk size, Update validation files and README stat

Pull Request - State: closed - Opened by dev-ansung about 7 years ago

#40 - More edits

Pull Request - State: closed - Opened by chadlaing about 7 years ago

#39 - Multiple copies detected at the same locus

Issue - State: open - Opened by mwhitesi over 7 years ago - 1 comment
Labels: good beginner task

#38 - FIX: eaeA in ref

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

#37 - UPDATE: shortnames to latest

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

#36 - Update superphy branch to new shortnames

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

#35 - Ectyper refactored

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

#34 - Ectyper refactored

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

#33 - Ectyper refactored

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

#32 - Ectyper refactored

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

#31 - Revert "Superphy" will move to new branch superphy

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

#30 - Superphy

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

#29 - bug fix: tmp_perc_id was rn tmp_perc_ln in 3d41f85

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

#28 - amr is working

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

#27 - Refactor sortMatches() & filterPredictions()

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