closest-features - manual page for closest-features
2.4.41+dfsg
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).
- 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.
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.