Amplicon sequence generation

[ThijsMaas]

Hi! This is Thijs from ENPICOM. We talked some weeks ago about including support for amplicon sequencing in ISS. We have developed and tested this functionality and would like your opinion on the changes proposed here.

This PR includes the following:

• A new argument --sequence_type which adds the 'amplicon' option to the default 'metagenomics'
  • This changes the read_start and read_end logic, for amplicon sequences the read pair is generated from the actual start and end of the sequence.
• Cleaned up some unused imports, variables, parameters, etc...
• Added new tests for amplicon sequencing mode

[HadrienG]

Merged #239 instead into devbranch