Merge branch 'check_for_ends' into juliema

Conflicts:
	sTRAM.pl
Merge branch 'juliema'
merge
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.