add `pyani dnadiff` subcommand about pyani

[kiepczi]

I have been working under the branch dnadiff.

Our main issue is that dnadiff returns 9 files for a single pairwise comparison. We do not want to generate that many files, especially when they are not needed. After my investigation, I managed to replicate the values for AlignedBases and AvgIdentity by running only scripts/programs that generate what we need.

To replicate the results, we need to generate 4 command lines:

1. nucmer to generate alignments with the --maxmatch parameter.
2. delta-filter to generate M-to-M alignments by calling the -m parameter.
   NOTE: Both commands 1 and 2 are different from the ones currently generated in the pyani anim subcommand.
3. show-coords to generate the .mcoords file needed to calculate AlignedBases and AvgIdentity.
4. show-diff to generate the .rdiff files needed for the AlignedBases calculation.

I have used the exact process implemented by dnadiff and successfully replicated the numbers for three separate test sets. You can find all the scripts and data here.

[widdowquinn]

Can we move the working branch for this to issue_424 to be consistent, please?

[widdowquinn]

See note in #422 regarding implementation with show-coords/show-diff.

[widdowquinn]

pyani dnadiff is something probably best reserved for the ground-up rebuild in pyani-plus - let's keep development for that project, not for this v0.3.

[kiepczi]

Can we move the working branch for this to issue_424 to be consistent, please?

As requested, the working branch for this issue was moved to issue_424.