NAME

       closest-features - manual page for closest-features 2.4.26+dfsg

DESCRIPTION

       closest-features

              citation:      http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
              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 <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>.

       --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.