This mode is used to tally the number of times sequences appear in a set of read files. Exact sequence comparison is performed. It is implemented by edu.cornell.med.icb.goby.modes.TallyReadsMode.java.
The following options are available in this mode
|Flag||Arguments||Required||Description||(-i|--input)||input||yes||Name of the compact input file.|
|(-o|--output)||output||yes||Base name of the filter file output (the resulting file will be the output basename given plus "-keep.filter").|
|--color-space||color-space||no||When this switch is provided, the sequence are expected in color-space.|