[ gia sort ]

Background

This subcommand will sort intervals from an input file.

Note: Chromosome Ordering

If named chromosomes are provided they will be sorted by the order in which they appear in the input file. In the future this will likely be lexicographically ordered.

Usage

See full arguments and options using:

gia sort --help

Sort an input BED

You can sort an input file with the following command:

gia sort -i <input.bed>

Sort a named input BED

If the chromosome names are non-integers you can run the following command:

gia sort -i <input.bed> -N