Add more tests for filtering mutations, more specific var-type options, option for controlling number of parallel threads (--jobs)

[matthuska]

Kind of a potpourri of a PR (sorry), containing extra testing of the feature filtering (skipping indels, trimming mutations at the ends of the genome) and solutions to issues with that which came up.

Also took this as an opportunity to add the ability to set the number of parallel threads that are used by the distance calculation (--jobs), which formerly had to be set using the OMP_NUM_THREADS environment variable. Lastly added a few extra checks to ensure that the program aborts in certain cases, like when there are duplicate sequence IDs in the input table.

[matthuska]

Closes #13

[denisbeslic]

breakfast --input-file output/nextclade.tsv --var-type nextclade_dna --id-col "seqName" --clust-col "substitutions" --sep2 ","
throws the following error

Clustering sequences
  Input file = output/nextclade.tsv
  Input file separator = '	'
  ID column = seqName
  clustering feature type = nextclade_dna
  clustering feature column = substitutions
  clustering feature column separator = ','
  max dist = 1
  minimum cluster size = 2
  trim start (bp) = 264
  trim end (bp) = 228
  reference length (bp) = 29903
  skip deletions = True
  skip insertions = True
  Input cache file = None
  Output cache file = None
Number of sequences: 10000
nextclade_dna
Skipping invalid feature: 'G210T'
Skipping invalid feature: 'C241T'
Skipping invalid feature: 'C1441T'
Skipping invalid feature: 'C3037T'
Skipping invalid feature: 'G4181T'
Skipping invalid feature: 'C6402T'
Skipping invalid feature: 'C7124T'
Skipping invalid feature: 'C8986T'
Skipping invalid feature: 'G9053T'
...
Traceback (most recent call last):
  File "X/.conda/envs/breakfast-dev/bin/breakfast", line 5, in <module>
    main()
  File "X/.conda/envs/breakfast-dev/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "X/.conda/envs/breakfast-dev/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "X/.conda/envs/breakfast-dev/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "X/.conda/envs/breakfast-dev/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "X/breakfast-dev/breakfast/src/breakfast/console.py", line 83, in main
    meta["feature"] = breakfast.filter_features(
  File "X/breakfast-dev/breakfast/src/breakfast/breakfast.py", line 160, in filter_features
    pos = int(submatch.group(1))
IndexError: no such group