Attempt to speed up filtering of secondary alignments
Attempt to speed up filtering of secondary alignments

The current code can sometimes slow down the alignment addition
process by several hours, probably depending on the size of the
megablocks. Huge amounts of time were being spent on
allocation/deallocation/search; this will hopefully cut that down
significantly.

benedictpaten/cactus,benedictpaten/cactus,benedictpaten/cactus,benedictpaten/cactus,benedictpaten/cactus