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.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-i|--input)inputyesName of the compact input file.
(-o|--output)outputyesBase name of the filter file output (the resulting file will be the output basename given plus "-keep.filter").
--color-spacen/anoWhen this switch is provided, the sequence are expected in color-space.