Parameters

-l Length of minimum match (25).

all readings with a match of this length are hits

-m Maximum vector length.

the length of the longest sequence to screen against (100000).

-i Input file of reading file names.

the file names of the readings to screen.

-I Input file of single reading to screen.

the file name of the reading to screen.

-s Input file of sequence file names.

the file names of the sequences to screen against.

-S Input file name of single sequence to screen against.

-p Passed output file of file names.

for the names of the readings that do not match.

-f Failed output file of file names.

for the names of the readings that match.

-t Test only mode.

results are only written to stdout and the experiment files are not altered.