.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH CLOSEST-FEATURES "1" "October 2018" "closest-features 2.4.35+dfsg" "User Commands"
.SH NAME
closest-features \- manual page for closest-features 2.4.35+dfsg
.SH DESCRIPTION
closest\-features
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citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
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https://doi.org/10.1093/bioinformatics/bts277
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version:
2.4.35 (typical)
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authors:
Shane Neph & Scott Kuehn
.PP
USAGE: closest\-features [Process\-Flags] <input\-file> <query\-file>
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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).
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For every element in <input\-file>, determine the two elements from <query\-file> falling
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nearest to its left and right edges (See NOTES below).
By default, echo the <input\-file>
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element, followed by those left and right elements found in <query\-file>.
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Process Flags:
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\fB\-\-chrom\fR <chromosome>
Jump to and process data for given <chromosome> only.
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\fB\-\-closest\fR
Choose the closest element for output only.  Ties go the left element.
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\fB\-\-delim\fR <delim>
Change output delimiter from '|' to <delim> between columns (e.g. '\et')
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\fB\-\-dist\fR
Print the signed distances to the <input\-file> element as additional
columns of output.  An overlapping element has a distance of 0.
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\fB\-\-ec\fR
Error check all input files (slower).
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\fB\-\-header\fR
Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
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\fB\-\-help\fR
Print this message and exit successfully.
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\fB\-\-no\-overlaps\fR
Overlapping elements from <query\-file> will not be reported.
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\fB\-\-no\-ref\fR
Do not echo elements from <input\-file>.
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\fB\-\-version\fR
Print program information.
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NOTES:
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If an element from <query\-file> overlaps the <input\-file> element, its distance is zero.
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An overlapping element takes precedence over all non\-overlapping elements.
This is true
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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.
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Overlapping elements may be ignored completely (no precedence) with \fB\-\-no\-overlaps\fR.
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.
.SH "SEE ALSO"
The full documentation for
.B closest-features
is maintained as a Texinfo manual.  If the
.B info
and
.B closest-features
programs are properly installed at your site, the command
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.B info closest-features
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should give you access to the complete manual.