SEECER version 0.1.3. + fix in replace_ids.cc for longer sequences

This is the pipeline version of SEECER 0.1.3 + a bug fix as found by
Nate. Namely in replace_ids.cc sequence lengths was set to max 265
otherwise seqfault, new max is 10000 but can be configure with
MAXSEQLENGTH.
small edits