Prelim support for cdna, and added -rip
Small bug in bowtie_2k handling fixed.
Better preliminary support for cDNA
Forgot to remove some print statements...
testing traceback
added traceback reporting to most of the runners.
a bit more output if cDNA results files are missing
Added handling for cDNA assemblies that exceed Newbler thresholds
isogroup header and checks for mislabeled PE files.
Merge remote-tracking branch 'origin/develop' into refactor
compare len, not the index...
converted to new structure
fixed typo
remove base since we are not using it yet
remove splitter
fixed issues from assembler rename
fixed config issues
initial refactor giving same results as develop
rename Extentions to contrib
remove print probes