Fixes `samtools sort` output to always be BAM

Closes #213.
Removes '(forces -S)' from samtools view -T|t usage
Updates documentation for `samtools view`

Adds all missing options to samtools man page under the
`samtools view` section.

Adds all missing options to `samtools view` usage and updates
notes to better reflect reality.

Closes #155. Although we should definitely split the samtools
man page into sub-pages for each command.