First pass at implementing strand information

This calculation, based on the best hit for tblastx, is not quite right.
velvet flag uses intermediate blast results from past runs
Merge branch 'master' into velvet
Revert "First pass at implementing strand information"

This reverts commit 960474090b15f5be6393a63e81c02205ca3275d7.
Merge pull request #31 from daisieh/velvet

Added -velvet flag (mostly for debugging): it redoes velvet assemblies on blast results generated from previous sTRAM runs.