pha4ge/hAMRonization

Issues

• nucleotide specific fileds are empty while importing AmrFinderPlus results based on nucleotide sequences

  #87 opened a month ago by m3hdad
  2

• [BUG] Generated output does not follow CSP rules

  #81 opened a month ago by remimestdagh
  1

• [BUG] - RGI bwt gene_mapping

  #84 opened 8 months ago by MicroSeq
  3

• Updating version support for starmar, amrfinderplus, kmerresistance - summarize output breaks

  #85 opened 4 months ago by lerminin
  4

• Request for Zenodo archive

  #82 opened a year ago by jasmezz
  0

• [BUG] `KeyError: 'reference_database_name'` when running summarize

  #80 opened 2 years ago by jfy133
  9

• PyPi not updated, 1.0.4 tarball reports version 1.0.3

  #78 opened 2 years ago by jfy133
  2

• Add fARGene

  #75 opened 2 years ago by jasmezz
  0

• Add xlsx output

  #73 opened 2 years ago by fmaguire
  1

• Flag to filter report for genomic/non-genomic audience

  #52 opened 3 years ago by fmaguire
  3

• Implementing logging and debug flag to simplify exception messages

  #56 opened 3 years ago by fmaguire
  2

• Update README

  #72 opened 2 years ago by cimendes
  0

• Add CONTRIBUTING.md

  #74 opened 2 years ago by cimendes
  0

• ORF_ID missing once RGI report hAMRonized

  #58 opened 2 years ago by SvetlanaUP
  1

• hamronize summarize - local variable 'parsed_report' reference before assignment

  #66 opened 2 years ago by cimendes
  3

• AMR Variant detection - Parsers to be updated

  #70 opened 2 years ago by cimendes
  1

• Flag overlapping ranges in hAMRonization

  #67 opened 2 years ago by fmaguire
  0

• Groot parser implementation

  #37 opened 2 years ago by cimendes
  5

• RgiIO.py: Typo in line 79

  #59 opened 2 years ago by SvetlanaUP
  1

• Genetic_variation_type

  #65 opened 2 years ago by jodyphelan
  1

• JSON/SALAD validation needs updated

  #27 opened 2 years ago by fmaguire
  2

• Extend schema(s) to include point mutation info

  #4 opened 2 years ago by dfornika
  1

• Obtain specification field data information from JSON schema

  #71 opened 2 years ago by cimendes
  1

• Fix issue of very similar runs falsely combining results in summary

  #61 opened 3 years ago by fmaguire
  0

• Using owl:equivalentClass to connect things semantically

  #34 opened 2 years ago by ddooley
  2

• Decide on a single 'authoritiative' schema format

  #6 opened 3 years ago by dfornika
  5

• staramr issue

  #54 opened 3 years ago by ewissel
  1

• help understanding resfinder run

  #57 opened 3 years ago by ewissel
  1

• Input file format and structure validation

  #39 opened 3 years ago by cimendes
  3

• Wrong Docker link

  #53 opened 3 years ago by iaconogi
  2

• Clearly specify which tool output files needing used

  #16 opened 3 years ago by fmaguire
  2

• Galaxy implementation

  #49 opened 3 years ago by fmaguire
  1

• add support for resfinder v4 output

  #44 opened 4 years ago by fmaguire
  0

• Sanity check parsers

  #18 opened 4 years ago by fmaguire
  2

• AMRfinder aminoacid reference lenght being saved in gene lenght field

  #42 opened 4 years ago by cimendes
  2

• Automated tests for parsers

  #19 opened 4 years ago by fmaguire
  4

• Dummy one-hit output for each tool

  #25 opened 4 years ago by fmaguire
  1

• Add custom error handling

  #32 opened 4 years ago by cimendes
  1

• Srst2 parser implementation

  #38 opened 4 years ago by cimendes
  1

• Summary options

  #35 opened 4 years ago by fmaguire
  1

• Point mutations for RGI + AMRFinderPlus?

  #30 opened 4 years ago by fmaguire
  2

• stderr output for empty files instead of crash

  #29 opened 4 years ago by fmaguire
  1

• Testing: flake8 linting shows errors & warnings but workflow step doesn't fail

  #5 opened 4 years ago by dfornika
  2

• Output options

  #24 opened 4 years ago by fmaguire
  0

• Reduce code duplication between parsers

  #22 opened 4 years ago by fmaguire
  1

• Global variable refactoring

  #21 opened 4 years ago by fmaguire
  0

• Programmatic use of parsers

  #23 opened 4 years ago by fmaguire
  0

• Type cleaning of fields needs implemented

  #20 opened 4 years ago by fmaguire
  0

• Add parser: Mykrobe

  #17 opened 4 years ago by fmaguire
  3

• Add Parser: resfinder

  #10 opened 4 years ago by raphenya
  1