Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

Regcollapse

Format

cg regcollapse ?options? region_file1 ...

Summary

Collapses overlapping regions in one (sorted) or more region files

Description

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.

Arguments

region_file1: region file
...: other region files

Options

-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

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