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closest-features - manual page for closest-features 2.4.26+dfsg



closest-features - manual page for closest-features 2.4.26+dfsg


citation: version: 2.4.26 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.
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')
Print the signed distances to the <input-file> element as additional columns of output. An overlapping element has a distance of 0.
Error check all input files (slower).
Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
Print this message and exit successfully.
Overlapping elements from <query-file> will not be reported.
Do not echo elements from <input-file>.
Print program information.
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.


The full documentation for closest-features is maintained as a Texinfo manual. If the info and closest-features programs are properly installed at your site, the command
info closest-features
should give you access to the complete manual.
June 2017 closest-features 2.4.26+dfsg