NAME
closest-features - manual page for closest-features 2.4.41+dfsg
DESCRIPTION
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).
- --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>.
- --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.
SEE ALSO
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.