Dark-matter

Added `--topReferenceIdsFile` option to `sam-reference-read-counts.py` to
allow the ids of the best-matching reference to be saved. Probably this
should save the FASTQ.

Improved `sam-reference-read-counts.py` output to not double-count reads
that fall into multiple categories and also to report how many reads match
references that don't match any earlier reported reference (to give some
idea of how many reads uniquely match references, where 'unique' means
didn't match any other reported reference (with more reads when `--sort` is
also used).

Added `--sort` option to `sam-reference-read-counts.py` to sort output
(i.e., matched references) by highest number of mapped reads.

`btop2cigar` now returns a generator that gives the individual parts of a
CIGAR string. Use `''.join(btop2cigar(...))` to get the full CIGAR string.
This is not backwards compatible, hence the major version number change.

Pass the `tmpChmod` argument to a call to `Bowtie2` for which it was
missing.

Added `--maxMatchingReads` to title fitering.

Added BAM file sorting to `make-consensus.py` so ivar primer trimming actually
works.