Refactored clustering code and new kmeans clustering criterion

[bricoletc]

This PR has two main goals:

• Continue the refactoring effort. This time on clustering code, placed in own source files, and added many more tests.
• Address part of #15 , by reducing ambiguous paths (distinct paths in prg with same sequence). From empirical tests on TB and Pf datasets, it does reduce this problem significantly, and improves downstream genotyping (in gramtools)

One important point is I've changed the command name prg_from_msa to from_msa; this way we call make_prg from_msa. This may be annoying because will need to change scripts using make_prg if we go ahead with this. I find it more descriptive and easier to type, but has to be weighed against changing calls in existing scripts/pipelines.

Added

• Unit tests for refactored kmeans clustering functions.
• Add failing clustering tests: all sequences very close getting grouped into clusters, sequences with three clusters getting grouped into two clusters
• New kmer clustering algorithm based on 'one-ref' principle, replacing inertia-halving criterion. Idea: if a group of sequences is similar to their majority sequence, do not need to be clustered. Similar defined via heuristic on %identity. This solves above failing cases and does not fail existing (eg integration) tests.

Modified

• Refactoring of kmeans clustering: take clustering code out of main AlignedSeq object and into own source file.
• Kmeans clustering split into more functions, for eg counting distinct kmers, producing kmer count matrix, extracting clusters, merging clusters.
• Place prg from msa source files in own from_msa directory
• Refactoring of AlignedSeq object: now called PrgBuilder; same for source file. Is clear it builds from msa as located in from_msa directory
• Rename prg_from_msa subcommand to from_msa for less redundancy: now call as make_prg from_msa

Test coverage

Goes from

Name                                   Stmts   Miss  Cover   Missing
--------------------------------------------------------------------
make_prg/__init__.py                      11      2    82%   13-14
make_prg/interval_partition.py           124      2    98%   67, 132
make_prg/io_utils.py                      99     79    20%   15-18, 36-39, 42-62, 67-126, 133-140, 153-178
make_prg/make_prg_from_msa.py            196     30    85%   70-74, 202-203, 290-297, 319, 343-374, 378-381
make_prg/prg_encoder.py                   40      0   100%
make_prg/seq_utils.py                     48      4    92%   77-84
make_prg/subcommands/__init__.py           2      0   100%
make_prg/subcommands/prg_from_msa.py      43     37    14%   9-68, 72-128
--------------------------------------------------------------------
TOTAL                                    563    154    73%

in current master

to

Name                                      Stmts   Miss  Cover   Missing
-----------------------------------------------------------------------
make_prg/__init__.py                          6      2    67%   6-7
make_prg/from_msa/__init__.py                 4      0   100%
make_prg/from_msa/cluster_sequences.py      141      0   100%
make_prg/from_msa/interval_partition.py     124      2    98%   67, 132
make_prg/from_msa/prg_builder.py            120     28    77%   67-71, 158-165, 187, 211-242, 246-249
make_prg/io_utils.py                        100     79    21%   16-19, 37-40, 43-63, 68-127, 134-141, 154-179
make_prg/prg_encoder.py                      40      0   100%
make_prg/seq_utils.py                        50      4    92%   81-88
make_prg/subcommands/__init__.py              1      0   100%
-----------------------------------------------------------------------
TOTAL                                       586    115    80%

in this branch