Build the package

Build the package with Nimble (included with Nim). The tool takes care of dependencies:

  $ nimble build covidphy_cli

Using the CLI

Classify a fasta sequence into haplogroups, returning a Json representation.

  covidphy_cli --fasta:path/to/file.fas
  covidphy_cli --f:path/to/file.fas
  cat path/to/file.fas | covidphy_cli

  -h --help    Show this message.
  -v --version Show the version.
  -f --fasta   The path to the fasta file. Only the first sequence of the
               file is going to be used.

A Json is returned, with the following schema:

 {"haplogroups": [
  "variants": ["T2C"...],