This mode is used to convert a compact alignment to counts. It is implemented by edu.cornell.med.icb.goby.modes.CompactAlignmentToCountsMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainputyesThe compact alignment file(s) to read as input.
(-o|--output)outputnoThe basename of the output counts.
(-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
--full-genomefull-genomenoIndicates that the query sequences were aligned to a full genome. When this argument is true, counts are calculated along each reference sequence and the full count histogram is output in compressed format (basename “.counts”). When this argument is false, the alignment is assumed to have been done to many short reference sequences, and counts are output in a tab delimited format, one for each reference sequence identifier.
--start-onlyn/anoWhen this switch is provided, will only accumulate start positions in the specified strand.
(-s|--strand-choice)strand-choicenoWhen provided with the –start argument, consider only start positions on the specified strand. Valid strand choices include {positive/forward, negative/reverse, both/either}.