Fixes printing of CLI errors.
Use .fai instead of .ann to fetch reference seqs.

This allows other aligners to be used, instead of just BWA, as
the .fai file is always generated, but the .ann file is unique
to the BWA index.
Allows BWA to be correctly executed on OSX.

This changes the command-line call to adhere to the stricter
requirements imposed by OSX, namely that options directly follow the
command name. To accomplish this, another class of parameters is added
(so-called positionals), which are added as the last part of the
command. Typically this will be the input/output files, as exemplified
by the following (where "input.bam" is the positional):

$ samtools view -h input.bam

This allows additional options to be set, without breaking the command.
Add initial bowtie2 support.