Compute Gap Between Feature Pairs

p3-feature-gap [options] <featurePairFile

This script reads in a list of feature pairs and computes the gap between the features. If the features are on different contigs or belong to different genomes, the gap will be listed as 2 billion. This behavior can be overridden with a command-line option.


There are no positional parameters.

The standard input can be specified using Input Options. The input column can be specified using Column Options. The following additional command-line options can be specified.


Value to return for an infinite gap (different contigs or genomes). The default is 2000000000.


Name or index of the column containing the ID of the second feature. The default is -1, which is the second-to-last column.