closest-features - manual page for closest-features 2.4.26+dfsg
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
- Process Flags:
- --chrom <chromosome>
- Jump to and process data for given <chromosome>
- Choose the closest element for output only. Ties go the
- --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
- Print this message and exit successfully.
- Overlapping elements from <query-file> will not be
- 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
- 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
programs are properly
installed at your site, the command
- info closest-features
should give you access to the complete manual.