cg regcollapse ?options? region_file1 ...


list regions collapse between region_file1 and region_file2


Collapses overlapping regions in one (sorted) or more region files, resulting in a region file (written to stdout) with non-overlapping regions covering the same total region as the source file(s). Overlaps between regions are cut at the overlap. Non overlapping regions keep the annotation (columns other than the ones indicated the region) of the original. Overlap regions get the annotation of the highest scoring region if a score column is available. If not, overlap regions are annotated with a (comma separated) list of the distinct values in the original annotations of the overlapping regions.

makes a new file with reg_ prepended to the original filename Removal of overlap can be done by taking only the highest scoring region (this is always done when score is available) or taking all regions in 1 line (if score is not available) for a field with then name num all values will be added use the -o option to collapse multiple files into one new file (the filename given with the option -o)


-o filename
write result to filename instead of stdout
-s scorefield
name of the column to use as scores.
-n numfield
name of a numfield: overlap regions will get the sum of the original values in this field as annotation


region file