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.