closest-features - manual page for closest-features 2.4.39+dfsg1
- citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
- 2.4.39 (typical)
- 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.
- 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.
|February 2021||closest-features 2.4.39+dfsg1|