Merge pull request #1 from andrewjpage/master

First version which scaffolds with sspace
Merge pull request #2 from andrewjpage/master

Gap filler
Merge pull request #3 from andrewjpage/master

abacas
Merge pull request #4 from andrewjpage/master

reference is not manditory
Merge pull request #5 from andrewjpage/master

use gap filler to improve assembly script
Merge pull request #6 from andrewjpage/master

user output directories
Merge pull request #7 from andrewjpage/master

Abacas support
Merge pull request #8 from andrewjpage/master

Abacas iterative
Merge pull request #9 from andrewjpage/master

descaffold an assembly
Merge pull request #10 from andrewjpage/master

redeclare var
Merge pull request #11 from andrewjpage/master

Improve documentation and add abacas
Merge pull request #12 from andrewjpage/master

promer
Separate role for unzipping files
Updated documentation for SGA preprocess module and added an _output_filename subroutine
SGA index and error correct stages added
Class to 'stick' SGA preprocess and error correction stages together
Added options to specify output directory if needed. Tests modified accordingly.
Main module and test
Filename bugs resolved.
Script to run sga