Fig 2. Auxiliary tools for building feature-rich pipelines.

a. Header verifies and modifies the.pairs format. b-d. Flip, select, and sample are for pairs manipulation. e-f. Scaling and stats are used for quality control. For scaling, we report scalings for all pairs orientations (+-, -+, ++, —) as well as average trans contact frequency. Orientation convergence distance is calculated as the last rightmost genomic separation that does not have similar values for scalings at different orientations. g-h. Restrict and phase are protocol-specific tools that extend pairtools usage for multiple 3C+ variants.