[ gia complement ]

Background

Similar to subtract, complement generates all the intervals that are not covered by the input set.

This is equivalent to subtracting the interval set from its span, which is an interval defined by the min and max interval of the set by chromosome.

Usage

See full arguments and options using:

gia complement --help

Default Behavior

(span)        s---------------------------------s
==========================================================
(input)       x------y     x-----y    x---------y
==========================================================
(complement)         y-----x     y----x

By default complement will return all intervals that are uncovered by the span of the incoming interval set.

The span of the interval set is calculated by chromosome.

gia complement -i <input.bed>

Note: Internal vs Complete Complement

The internal complement of a set necessarily excludes the the chromosomal start to the span start and the span end to the chromosomal end.

All other potential intervals are included.