Zip the final output file produced after error correction
Expect full path to file for gzipping. Do not try to get abs path here
Comments added
Revert back to getting absolute path of input file
Added ability to take in an output filename rather than default
Move preprocessed file into current temporary directory before it gets deleted
Added a subroutine to return intermediate filename for preprocessed results
Added test to check for intermediate preprocessed results in tmp directory
Removed duplicate d parameter. Used i for disk parameter for sga indexing
Use the --learn option as default in sga correct
Corrected the path of the zip file produced
Do not use the --permute-ambiguous flag with preprocess by default
Merge branch 'add_sga_step' of github.com:nds/assembly_improvement into add_sga_step
Change quality trim to 20 and do not do quality filtering
Changed -d parameter for indexing to 1000000
Merge pull request #14 from nds/add_sga_step

Add sga error correction step before running velvet
Bug fixed. Was still referring to quality filter when trying to run preprocess
Removed redundant variable declaration
Merge pull request #15 from nds/add_sga_step

Add sga step