Check that paired reads have the same QNAME

This detects desynchronised input files, which occasionally happens
due to user error or system failure.

Checking the names just after printing them has no real performance
implications because the strings are already in cache.  (It might
be better to check while reading the input, but that would be more
complicated in the two-input-files case.)
Complain when bwa mem is given too many filenames

Reads in extra .fq filenames beyond "bwa mem index one.fq two.fq"
will not be aligned, so complain about such invalid usage instead.
Reformat note for 80 columns, and fix typo
Merge pull request #19 from jmarshall/check-qnames

Check that input files are name-sorted and the names of paired reads match
Merge branch 'master' into clip2