Added flattenfasta (same as sortfasta but without sorting)
Calculates percent coverage of all .best.fasta files in a directory.

Assumes that the reference fasta seqs are available and appropriately
named.
Revert "Calculates percent coverage of all .best.fasta files in a directory."

This reverts commit c26a5c494e7b47bfff15f33206eaf33a7470d85a.
Original version of Julie's code (for posterity!)
Now we can look at a nice diff between the two versions.
Merge pull request #67 from juliema/percent_coverage

Percent coverage: fixes issue #41