This mode is used to convert annotations to counts. Annotations can be used to represent segments of the reference sequences. This is can used to represent boundaries of exons on the chromosome sequences or the boundary of any other chromosomal region(s). This mode converts annotation files to the count format, setting count within the regions defined by the annotations to 1 and zero outside of the annotated regions. It is implemented by edu.cornell.med.icb.goby.modes.AnnotationsToCountsMode.java.
The following options are available in this mode
|output||no||The name of the output basename to write the count archive. Default value: output-basename|
|flanking-size||no||Extend captured regions by this number of bases on either side. Default value: 100|
|input||yes||The basenames of the input alignments|
|n/a||no||Verbose. For instance, reports when annotation segments are joined because they overlap. Default value: FALSE|