Bug in Tophat when --mate-inner-dist + --mate-std-dev < 0

[Nicklas Nordborg]

This was initially thought to be a problem with an incorrect value for the --mate-inner-dist parameter due to lot of clipping when sequencing 2x150 reads (see #1336 and #1335).

However, investigations shows that there is a bug in Tophat when marking aligned pairs as a proper pairs that is triggered when the --mate-inner-dist parameter is negative and --mate-std-dev is less than abs(--mate-inner-dist). For example:

--mate-inner-dist -80 --mate-std-dev 79 // will trigger the bug
--mate-inner-dist -79 --mate-std-dev 79 // works

To avoid triggering the bug we should make sure that the --mate-inner-dist parameter always is large enough.