further optimisations which reduce num of allocs

Basically trying to remove the number of calls to alloc by preserving
the score array for the duration of the call to find_best_match
[scythe.c] fix to fclose output_fp w/ -o option
update tests w/ optimised score_sequence API
Merge pull request #18 from kdmurray91/optimised

Further optimisations
Merge pull request #19 from kdmurray91/fix-fclose

Call fclose on output_fp when -o option is given
version bump; removed paper, this will go into separate repository