closest-features1

Overview

closest-features

citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract

https://doi.org/10.1093/bioinformatics/bts277

version:

2.4.41 (typical)

authors:

Shane Neph & Scott Kuehn

USAGE: closest-features [Process-Flags] <input-file> <query-file>

All input files must be sorted per sort-bed. The program accepts BED and Starch file formats May use '-' for a file to indicate reading from standard input (BED format only).

For every element in <input-file>, determine the two elements from <query-file> falling

nearest to its left and right edges (See NOTES below).

By default, echo the <input-file>

element, followed by those left and right elements found in <query-file>.

Process Flags:

--chrom <chromosome>

Jump to and process data for given <chromosome> only.

--closest

Choose the closest element for output only. Ties go the left element.

--delim <delim>

Change output delimiter from '|' to <delim> between columns (e.g. '\t')

--dist

Print the signed distances to the <input-file> element as additional columns of output. An overlapping element has a distance of 0.

--ec

Error check all input files (slower).

--header

Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.

--help

Print this message and exit successfully.

--no-overlaps

Overlapping elements from <query-file> will not be reported.

--no-ref

Do not echo elements from <input-file>.

--no-query

Do not echo elements from <query-file>.

--version

Print program information.

NOTES:

If an element from <query-file> overlaps the <input-file> element, its distance is zero.

An overlapping element takes precedence over all non-overlapping elements.

This is true

even when the overlapping element's edge-to-edge distance to the <input-file>'s element is greater than the edge-to-edge distance from a non-overlapping element.

Overlapping elements may be ignored completely (no precedence) with --no-overlaps. Elements reported as closest to the left and right edges are never the same. When no qualifying element from <query-file> exists as a closest feature, 'NA' is reported.