This mode is implemented by edu.cornell.med.icb.goby.modes.TallyBasesMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainputyesThe count basename to use as input.
(-o|--output)outputyesThe file where base tallies will be written.
(-r|--include-reference-names)include-reference-namesnoWhen provided, only write counts for reference identifiers listed in this comma separated list. To process only counts for chromosome 19 and 1, if sequences are identified by 1 and 19, use: --include-reference-names 1,19
(-a|--alternative-count-archive)alternative-count-archivenoSpecify an alternative count archive within the basename. The default is to use the count archive that ends in ".counts" (equivalent to -a counts).
(-g|--genome)genomeyesGenome in fasta format (extension .fa or .fa.gz) or compact format (extension .compact-reads).
(-c|--genome-cache)genome-cachenoFilename where a random access binary cache of the genome will be written. The default cache filename is derived from the genome command line argument.
--offsetoffsetnoThe position offset of the second basename relative to the first. The offset is added to the position of counts in the second count archive. When auto, offsets from -10 to 10 are scanned and the one which results in the best agreement between the two counts archive is used.
--cutoffcutoffnoThe fold-change cutoff to report a position.
--sample-ratesample-ratenoThe rate at which counts are sampled form the genome. 100% will extract bases for all positions that match the fold-change cutoff, 10% will reduce the number of positions reported by 10.