SILO input transformer

[fengelniederhammer]

Integrate and finalize the SILO input transformer.

It is a follow up to #562. This issue removes the TSV/FASTA input format from the SILO code (and leaves SILO only with the NDJSON input). The SILO input is a separate tool that can translate the TSV/FASTA format to the NDJSON input, so that SILO still "supports" both formats (eventually by running the input transformer first).

This is a list of tasks that need to be done (not necessarily in a good order for implementation):

• SILO input transformer: Integrate the code into the SILO repository.
  • Currently it's in this private repo: https://github.com/fengelniederhammer/SILO-input-transformer
• SILO input transformer: add logging
• SILO input transformer: Allow compressed input files
• SILO input transformer: compress sequences in intermediate steps
  • to reduce the amount of data that needs to be transferred between the program and the disc.
• SILO input transformer: allow command line arguments
  • especially specifying where the config is located and whether to keep intermediate files (and maybe the log level)
• SILO input transformer: error messages
  • We already have error handling, but the errors might be hard to understand for users.
• SILO input transformer: add more unit tests
• SILO input transformer: add some e2e tests
• SILO input transformer: parallelize where possible
• SILO input transformer: support SAM files
• SILO input transformer: include insertions
  • to do: think about whether we want to keep the old input format
• SILO input transformer: clean up temp folders
• SILO input transformer: accept empty fasta files
  • currently the fasta parser complains when a fasta file is empty.