[ gia merge ]

Background

This subcommand will merge all overlapping and bordering intervals within the input set.

It can accept either a presorted input (which can be streamed) or an unsorted input which will first be sorted in-place before merging.

Usage

See full arguments and options using:

gia merge --help

Default Behavior (Inplace)

(e)                    q----r
(b)      k----l
(a)    i----j
(c)           l----m
(d)                  o----p
===============================
(1)    i-----------m
(2)                  o------r

This will merge all overlapping and bordering intervals into their sub-spans.

It does not assume presorted input and will sort the input inplace on load.

gia merge -i <input.bed>

Streamable Input

(a)    i----j
(b)      k----l
(c)           l----m
(d)                  o----p
(e)                    q----r
===============================
(1)    i-----------m
(2)                  o------r

This will merge all overlapping and bordering intervals into their sub-spans.

This assumes presorted input and will have undefined behavior is input is not-sorted.

gia merge -i <input.bed> -S