Complete reimplementation of RnaChipIntegrator to unify internal algorithms, simplify usage and substantially update the documentation. No distinction is now made between 'summits' and 'peaks'; the same algorithm is applied in each case. The program always finds the nearest features to each peak, and vice versa. The same distance cutoff and maximum number of hits are applied to both and can be specified using the --cutoff and --number options. By default nearest distances between peaks and features are calculated from the TSS of the feature to whichever of the peak edges are closer; alternatively distances can be calculated between the nearest pair of peak/feature edges by specifying the --edge=both option. Any differential expression flags in the input features file are ignored unless the --only-DE option is specified, in which case only the differentially expressed features are considered in the analyses. By default each peak/feature pair is reported on a separate line; the --compact option reports all nearest features/peaks on a single line of output. Excel output is only produced if the --xls option is specified; summary output is only produced if --summary is specified. The rearrange_columns.py utility has been dropped.