phac-nml/staramr

Issues

• `np.unicode_` was removed in the NumPy 2.0 release

  #213 opened 5 months ago by sgsutcliffe
  1

• Genome length not within range

  #214 opened 5 months ago by joao1980
  3

• Change to Phenotype Request

  #215 opened 5 months ago by sgsutcliffe
  0

• Adding more databases

  #209 opened 6 months ago by joao1980
  1

• Add to GRDI-AMR.com

  #211 opened 6 months ago by chapb
  2

• CGE phenotype not populated for E. faecium pbp5 when all essential mutations are present

  #210 opened 7 months ago by lerminin
  1

• A Full Set of pbp5 Ampicillin Mutations are on the Threshold of the Default Percent Identity

  #208 opened 10 months ago by emarinier
  0

• Dashes in updated pointfinder db cause crash

  #207 opened 10 months ago by lerminin
  0

• AttributeError: type object 'object' has no attribute 'dtype'

  #206 opened a year ago by siupenyau
  4

• conda install gets an old version which does not run well

  #205 opened a year ago by splaisan
  4

• docker image v0.8.0 does not accept --user

  #204 opened a year ago by splaisan
  3

• Add option to specify database path

  #200 opened a year ago by pimarin
  4

• Update MLST references in README

  #203 opened a year ago by emarinier
  0

• different percent identity/alignment length for identical sequences on opposite strands

  #201 opened a year ago by lerminin
  5

• ERROR: the local id is too long or OSError: [Errno 39] Directory not empty: 'input-genomes'

  #202 opened a year ago by elina2410
  3

• Update StarAMR documentation

  #191 opened a year ago by apetkau
  1

• Update Plasmidfinder DB

  #188 opened a year ago by emarinier
  1

• Add PointFinder "Required_mut" column to pointfinder.tsv results

  #195 opened a year ago by apetkau
  1

• AttributeError: 'float' object has no attribute 'split'

  #175 opened a year ago by vappiah
  5

• an unexpected keyword argument "inplace" and can't out the "results.xlxs"

  #184 opened a year ago by Yovelaaa
  3

• cant run staramr

  #181 opened a year ago by Hedi65
  3

• Include CGE-Predicted Phenotypes for PointFinder results

  #170 opened a year ago by apetkau
  3

• Error: multiple matches for gene=gyrA

  #174 opened a year ago by stanikae
  3

• Include drug resistances from PointFinder in StarAMR report

  #165 opened a year ago by apetkau
  1

• staramr db info error: [Errno 2] No such file or directory: 'mlst'

  #166 opened a year ago by FeMa94
  4

• Available MLST scheme list is out of date

  #168 opened a year ago by eam12
  4

• Change sensitive to susceptible in report

  #164 opened a year ago by apetkau
  1

• PlasmidFinder database enterobacteriaceae no longer an option

  #169 opened a year ago by eam12
  1

• Duplicated resfinder hits with update to database

  #180 opened 2 years ago by kimyoungw
  5

• The plasmidfinder.tsv shows that there is no plasmid present

  #178 opened 2 years ago by qianxin-kxy
  4

• ERROR: ('Error, plasmidfinder database type [{}] is either incorrect or plasmidfinder database not installed properly', 'enterobacteriaceae')

  #177 opened 2 years ago by qianxin-kxy
  2

• start and end position

  #176 opened 2 years ago by vappiah
  1

• Include CGE-Predicted Phenotype results in summary results

  #171 opened 2 years ago by apetkau
  0

• Update Galaxy STARamr and add a text option for pointfinder species

  #161 opened 2 years ago by pimarin
  4

• Bioconda channel order

  #162 opened 2 years ago by lenorakepler
  2

• better error messages for empty results list

  #155 opened 2 years ago by bgruening
  4

• Some plasmidfinder blast results causing staramr to crash

  #158 opened 2 years ago by apetkau
  0

• Can;t install staramr, blast not found.

  #141 opened 3 years ago by Abelcanc3rhack3r
  2

• update pointfinder database to include all species

  #152 opened 2 years ago by pimarin
  11

• Update staramr databases

  #148 opened 3 years ago by apetkau
  1

• Change strict restriction on PointFinder organisms to be a warning

  #147 opened 3 years ago by apetkau
  2

• ModuleNotFoundError: No module named 'staramr'

  #142 opened 3 years ago by neelam19051
  6

• bioconda dependencies

  #133 opened 3 years ago by pmenzel
  2

• toList error type

  #136 opened 3 years ago by safinaARK
  2

• Customize threshold for hit detection

  #143 opened 3 years ago by andreaniml
  2

• Genome length error

  #140 opened 3 years ago by XtineLiu
  2

• N50 < 10000

  #135 opened 3 years ago by MarcelaHer
  1

• neisseria gonorrhoeae point finder database

  #139 opened 3 years ago by peflanag
  3

• AttributeError: 'NoneType' object has no attribute 'tolist'

  #134 opened 3 years ago by arif-tanmoy
  3

• aac(6')-Iaa excluded

  #132 opened 3 years ago by Andrea-SS
  2