cov-lineages/scorpio

Issues

• Scorpio: Many BA.4/5 misclassified as BA.2* because "Probable Omicron (BA.2-like)"

  #47 opened 2 years ago by corneliusroemer
  26

• hundred XM genomes called as 'Unassigned' or as BA.1

  #46 opened a year ago by akifoss
  5

• XBB.1 misclassified as XBB in Singapore in samples after 2022-10-10

  #49 opened 2 years ago by mg14
  0

• Pangolin v1.12 as used by GISAID misclassifies a lot of true BA.5* as BA.2*

  #48 opened 2 years ago by corneliusroemer
  2

• Scorpio overriding UShER calls for XD recombinants

  #45 opened 2 years ago by SVN-PhD
  1

• Make scorpio multithreaded

  #37 opened 3 years ago by rmcolq
  0

• Allow for a rule with more flexibility for indels

  #29 opened 3 years ago by rmcolq
  2

• Giving input file without `-i` causes stack trace

  #41 opened 3 years ago by rambaut
  0

• Allow a constellation to have different levels of rules for e.g. probable cases rather than certain cases

  #35 opened 3 years ago by rmcolq
  0

• Allow mutation strings to have comments at the end (if this doesn't work already)

  #36 opened 3 years ago by rambaut
  1

• Add check that scorpio file is compatible with current scorpio version

  #40 opened 3 years ago by rambaut
  0

• scorpio overriding AY.4.2 to B.1.617.2 on very few Ns

  #32 opened 3 years ago by mcroxen
  12

• fastq as input data

  #33 opened 3 years ago by carlottaolivero
  1

• Do a 'union' haplotype of multiple definition files.

  #26 opened 3 years ago by rambaut
  1

• Enable multiple constellation files for the same "constellation"

  #30 opened 3 years ago by rmcolq
  1

• Add a list of problematic sites and provide a warning if one comes back as reference

  #9 opened 3 years ago by rmcolq
  1

• For `haplotype` command only use one directory of constellation files.

  #25 opened 3 years ago by rambaut
  2

• Add option to include additional mutation calls from a mutations CSV when classifying

  #6 opened 3 years ago by rmcolq
  0

• Allow mutations to be specified on command line for scorpio haplotype

  #22 opened 3 years ago by rmcolq
  0

• Scorpio version reporting 0.3.5 incorrectly (?)

  #21 opened 3 years ago by jacaravas
  1

• Mutation information

  #18 opened 3 years ago by santoshe1
  2

• Bug in scorpio

  #15 opened 3 years ago by animesh-workplace
  9

• Add option to output other labels (i.e., --who-label and --phe-label

  #11 opened 3 years ago by rmcolq
  0

• Handle changed constellation labels

  #12 opened 3 years ago by rmcolq
  0

• Improve deletion handling

  #13 opened 3 years ago by rmcolq
  0

• Create an optional interspersion statistic

  #10 opened 3 years ago by rmcolq
  0

• CDS orf1a at position 741 is L, but reference sequence has F

  #8 opened 3 years ago by tseemann
  6

• Enable protein based mutation definitions e.g. NSP1

  #7 opened 3 years ago by rmcolq
  0

• Allow outgroups to be specified when running `define`

  #3 opened 3 years ago by rmcolq
  0

• Add support score when haplotyping/classifying

  #1 opened 3 years ago by rmcolq
  0

• Use support when classifying to choose the constellation with best support

  #2 opened 3 years ago by rmcolq
  0

• In `define` output intermediates in nice format

  #4 opened 3 years ago by rmcolq
  0

• Add command line args for intermediate thresholds for `define`

  #5 opened 3 years ago by rmcolq
  0