Provided by: bedops_2.4.35+dfsg-1_amd64
closest-features - manual page for closest-features 2.4.35+dfsg
closest-features citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract https://doi.org/10.1093/bioinformatics/bts277 version: 2.4.35 (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>. --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.
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.