Merge branch 'juliema'
Merge branch 'juliema' into check_for_ends
Merge branch 'check_for_ends'
added flag "velvet"

If specified, runs velvet assembly only on the filtered read
intermediate files from a previous run.
Revert "added flag "velvet""

This reverts commit 179a5412808c442b390232fd70c995b311330bbc.
Fixes #17.
Merge pull request #29 from daisieh/p17

Fixes #17.
Fixes #23

Quits if a contig contains both the beginning and end of the target if
the -complete flag is specified; otherwise reports contigs that contain
both the start and end of the target at the end.
Merge pull request #30 from daisieh/p23

Fixes #23
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.