Dark-matter

Make `fasta-diff.sh` handle compressed files, exit with diff's status,
and make it possible to pass command line options through to diff.

Added `bin/fasta-diff.sh` as a quick diff function that knows about
FASTA/FASTQ files. Added `bin/fasta-join.py` as a helper function for
`bin/fasta-diff.sh`.

Fix [636](https://github.com/acorg/dark-matter/issues/636) in which SAM file
parsing threw an exception when an unmapped sequence with no CIGAR string
occurred in a SAM file (this can happen when running `bowtie2 --all`).

Fixed thinko in 3.0.42.

[Pysam issue 716](https://github.com/pysam-developers/pysam/issues/716)
wasn't solved the way we hoped it would be, so now the `filter-sam.py`
command always passes the template of the original SAM file to the
constructor for the new file. As a result, the new file will have `SN`
entries for all the original sequences, even when `--referenceId` is passed
to `filter-sam.py` to restrict output to a specific set of reference ids.

Added `--showDiffs` option to `bin/compare-sequences.py`.