Fig. 1

Pgltools Implementation (a) An example of sorted, single locus bed file entries from a file sorted by start position. As entry 1 overlaps entry 3, entry 2 must also overlap entry 3. (b) A pictorial representation of PGL entries in a sorted PGL file where non-sequential PGL entries overlap. Loci are shown as blocks, with dashed lines connecting the paired-loci comprising a single entry. Both loci A and B in PGL entries 1 and 3 overlap, and both loci in PGL entries 2 and 4 overlap. (c) A flowchart of the overlap function shared between many operations in pgltools. File 2 has N-1 entries. File 2 is iterated by the File2-index i. File2[i] is a PGL entry for any 0 ≤ i < N. Throughout the algorithm, PGL entries from File 2 must be checked multiple times. Therefore, to reduce the number of comparisons performed by pgltools, the Recheck Index is used to store the index at which the previous overlap iteration began. When the ends of both files are reached, the algorithm ends