Remove some cruft. Set STAR to be the default.
Fix for Tophat with single-end reads and final BAMfile naming.

In single-end mode, fixing the unmapped reads with single-end
reads was causing all reads to be discarded. Also the
final BAMfile was getting linked to from the align directory and
not the subdirectory of the alignment below it.
Put symbolic links in the correct directory.

These were inadvertantly linked in the toplevel align directory
instead of the lane-specific subdirectory.
Add a singleend tag for testing single-end data.
Fix for failure on very low coverage samples.

If there is not enough to call coverage anywhere, just
return None.
Remove trailing /1 from this single-end dataset.