This mode suggests how to slice an alignment by position to yield roughly equally sized slices.  It is implemented by
edu.cornell.med.icb.goby.modes.SuggestPositionSlicesMode.java. Since Goby 1.9.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainputyesThe alignment basenames for which slices are needed.
(-o|--output)outputnoThe file where slices definitions will be written (tab delimited: targetIdStart %positionStart start:(ref,pos) targetIdEnd %positionEnd end:(ref,pos).
(-a|--annotations)annotationsnoWhen provided, filename to Goby annotation file. Slices are generated such that no slice would split the external boundaries of an annotation element.
(-n|--number-of-slices)number-of-slicesnoThe number of slices to produce. Default value: 10
(-b|--number-of-bytes)number-of-bytesnoThe approximate number of compressed bytes to put in each slice. Default value: 50000000
--modulomodulonoModulo for slicing positions. Large numbers require less memory and result in coarser, potentially less balanced slices. Default value: 1000000
--restrict-per-chromosomen/anoWhen this switch is provided, slices will be restricted to start and end on the same chromosome. Default value: FALSE
-xdynamic-optionsnoSet a dynamic option, in the format classname:key=value. Classname is the the name of the class that exposes the option (short class name without package), key identifies the option to change and value is the new value for the option.