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.