Merge pull request #1 from andrewjpage/master

Basic wrappers
Merge pull request #2 from andrewjpage/master

use time as object not string
Merge pull request #3 from andrewjpage/master

genus
Merge pull request #4 from andrewjpage/master

uniq temp directory
Merge pull request #5 from andrewjpage/master

temp directory type
Merge pull request #6 from andrewjpage/master

Create seq files once
Merge pull request #7 from andrewjpage/master

allow genus to be passed into cmd
Merge pull request #8 from andrewjpage/master

dont overwrite gene name if its set
Merge pull request #9 from andrewjpage/master

dont over write with blank gene name
Merge pull request #10 from andrewjpage/master

limit to 1 cpu for pipeline
Merge pull request #11 from andrewjpage/master

enable rfam by default
Merge pull request #12 from andrewjpage/master

exclude aragorn end tag
Merge pull request #13 from andrewjpage/master

fix infernal coord system
Merge pull request #14 from andrewjpage/master

take sequence id from infernal results
Merge pull request #15 from andrewjpage/master

fasta file of extracted genes
Merge pull request #16 from andrewjpage/master

allow qualifiers to be chosen
Merge pull request #17 from andrewjpage/master

move cmscan to class and test
Merge pull request #18 from andrewjpage/master

use cmobj
Merge pull request #19 from andrewjpage/master

calc files with and without hits
Merge pull request #20 from andrewjpage/master

number of features in cmscan obj