Fig. 2

The operations of pgltools. PGL entries from file one are shown in various shades of blue, PGL entries from file two are shown in orange, and windows are shown in yellow (see legend at bottom right). All resulting outputs are shown below dashed lines, with novel entries shown in green and original entries shown in their original color. (a) The intersect operation finds overlapping paired-genomic-loci between two PGL files and returns the overlapping regions. (b) The merge operation combines overlapping paired-genomic-loci within a single PGL file. (c) The subtract operation returns the PGL entries from file one with the PGL entries from file two removed. (d) The window operation returns the PGL entries that fall completely within a specified genomic region. (e) The coverage operation returns the number of PGL entries from file two that overlap each PGL entry in file one. (f) The closest operation returns the closest PGL entry from file two for each PGL entry in file one. (g) The intersect1D operation returns PGL entries from file one that overlap regions in a bed file. (h) The closest1D operation returns the closest region from a bed file for each PGL entry in file one. (i) The subtract1D operation returns the PGL entries from file one with the regions from a bed file removed