lenaschimmel/sc2rf

Issues

• Bug/question with --force-all-parents --clades all

  #35 opened 2 years ago by MarieLataretu
  3

• Release a version

  #5 opened 3 years ago by erinyoung
  5

• Bridging the gap between sc2rf result and Pangolin X* lineages

  #34 opened 2 years ago by bioinforME
  0

• How to interpret BA.4/BA.5 list of mutations

  #32 opened 3 years ago by jpflorido
  0

• GISAID XT recombinant not detected by sc2rf

  #31 opened 3 years ago by BenjaminDelisle
  4

• Option to ignore shared substitutions

  #30 opened 3 years ago by ktmeaton
  0

• Terminal Ns not recognized as missing

  #29 opened 3 years ago by ktmeaton
  1

• --csvfile option does not work

  #28 opened 3 years ago by think-o
  2

• Find and use better source for typical mutations of lineages

  #4 opened 3 years ago by lenaschimmel
  14

• Crash related to tdqm

  #27 opened 3 years ago by lenaschimmel
  4

• Make tool pip-installable

  #3 opened 3 years ago by corneliusroemer
  4

• BUG: Problem using covSpectrum mutation share - Ns are treated as reference

  #23 opened 3 years ago by corneliusroemer
  10

• ENH: provide output optionally as csv/tsv for automated analysis/sharing

  #19 opened 3 years ago by corneliusroemer
  28

• ENH: Sort by breakpoint

  #26 opened 3 years ago by corneliusroemer
  0

• ENH: Output full internal representation of analysis result for sharing without need for recomputation

  #22 opened 3 years ago by corneliusroemer
  2

• ENH: Accept MAPLE file as alternative to fasta

  #24 opened 3 years ago by corneliusroemer
  0

• Deltacrons with NSP3 breakpoint

  #8 opened 3 years ago by ktmeaton
  17

• ENH: Differentiate between clade defining mutations and optional mutations

  #15 opened 3 years ago by corneliusroemer
  3

• Have a look at the Δm, n, 2 statistic for breakpoint detection

  #21 opened 3 years ago by lenaschimmel
  0

• Add relevant primer bed files and make sure the bed format is correctly interpreted

  #20 opened 3 years ago by lenaschimmel
  0

• Issues with VT / ANSI color codes, especially on Windows/Ubuntu

  #2 opened 3 years ago by lenaschimmel
  1

• ENH: show progress bar, say how many files were read in, how processing is going

  #16 opened 3 years ago by corneliusroemer
  2

• ENH: repeat gene legend every say 30 samples in case of long list

  #18 opened 3 years ago by corneliusroemer
  2

• ENH: add spaces between genes rather than every 5 mutations

  #17 opened 3 years ago by corneliusroemer
  1

• ENH: Allow tool to run in a web browser

  #13 opened 3 years ago by corneliusroemer
  4

• Q: Why show all donors not just the relevant ones?

  #14 opened 3 years ago by corneliusroemer
  6

• Way to pipe results to png, txt files

  #9 opened 3 years ago by bdelavan
  7

• Fix or remove 21I and 21J

  #10 opened 3 years ago by lenaschimmel
  11

• Allow more file formats and/or access methods, i.e. Auspice v2 dataset JSON from nextstrain URLs

  #12 opened 3 years ago by lenaschimmel
  0

• Write documentation on how to interpret the output

  #11 opened 3 years ago by lenaschimmel
  0

• TypeError: unsupported operand type(s) for |: 'dict' and 'dict'

  #7 opened 3 years ago by arodzh-sudo
  1

• Python version requirement 3.9

  #6 opened 3 years ago by benkraj
  2