Dark-matter

Added printing of reference lengths to `bin/sam-reference-read-counts.py`.
Changed the `--sort` option of that script to `--sortBy`. Added options to
stop printing references once they either have no reads mapped to them or
the number of new reads mapped to them ("new" as in not already mapping to
an earlier reference) falls to zero.

Added `fasta-split.py` command to split a FASTA/Q file into multiple files,
each containing a given number of sequences. Added `dark/utils.py` function
`take` to repeatedly yield lists of a given number of things from an
iterable.

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.