CAST-genomics/haptools

docs: updates ahead of v0.1.0

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some changes we should make to the docs ahead of our new haptools release:

  • describe where the example and test files are
  • mention that hex codes can be provided to karyogram
  • explain how the --verbosity flag works on the front page of our docs
  • motivate the need for a .hap file format
  • change default verbosity mentioned in __main__.py. Currently it says "only errors"
  • more clearly link to files for simgenotype in the docs for it?
  • tone down language about automatically supporting 1000G files
    say that we support 1000G file formats, but do not implement anything within haptools that specifically supports 1000 Genomes
  • fix the link to the beagle map files. I think it's broken
  • on the front page, consider linking to the github-hosted pipeline image instead of linking from google drive? to reduce chance of the image not loading