Remove old pre-5.10 way of calling coverage-stats.
Whitespace.
Call TophatAlignmentStats directly.
Unpin perl version in #! lines.
Remove obsolete comment.

This is already directly called.
Call commands directly.
Switch to direct command calls.
Whitespace.
Call command directly.
Remove references to /usr/bin/perl.

`gmt` should use the `genome-perl` now, which should be at least 5.10.
Remove old comment.

This was updated to call directly in
53401d1e1fa998bc1d66d125d6f65dea375dd0de.
Update comments to remove old advice.
Call ref-cov directly.
Use the current version of genome-perl.
Whitespace.
Call command directly.
Remove empty __END__.
Remove obsolete comment.
Remove obsolete comment.
Remove obsolete comments.