NAME

       positionDB - management of posDB files

SYNOPSIS

       positionDB  [-mersize  k]  [-merskip  k]  [-use a-b,c] [-merbegin b] [-merend e] -sequence
       s.fasta -output p.posDB

       positionDB -dump datafile

       positionDB -test1 sequence.fasta

       positionDB -test2 db.fasta sequence.fasta

OPTIONS

   Building an image
       -mersize k
              The size of the mers, default=20.

       -merskip k
              The skip between mers, default=0

       -use a-b,c
              Specify which sequences to use, default=all

       -merbegin b
              Build on a subset of the mers, starting at mer #b, default=all mers

       -merend e
              Build on a subset of the mers, ending at mer #e, default=all mers

       -sequence s.fasta
              Input sequences.

       -output p.posDB
              Output filename.

   Dumping information about an image
       -dump datafile.posDB

   Running sanity tests
       -test1 sequence.fasta
              Tests if each and every mer is found in the positionDB.  Reports if it doesn't find
              a mer at the correct position.  Doesn't report if table has too much stuff.

       -test2 db.fasta sequence.fasta
              Builds  a  positionDB  from  db.fasta,  then  searches  the  table  for each mer in
              sequence.fasta.  Reports all mers it finds.

              This is a silly test and you shouldn't do it.

SEE ALSO

       existDB(1), meryl(1)