.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH BEDOPS "1" "October 2018" "bedops 2.4.35+dfsg" "User Commands"
.SH NAME
bedops \- manual page for bedops 2.4.35+dfsg
.SH DESCRIPTION
bedops
.IP
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
.IP
https://doi.org/10.1093/bioinformatics/bts277
.TP
version:
2.4.35 (typical)
.TP
authors:
Shane Neph & Scott Kuehn
.IP
USAGE: bedops [process\-flags] <operation> <File(s)>*
.IP
Every input file must be sorted per the sort\-bed utility.
Each operation requires a minimum number of files as shown below.
.IP
There is no fixed maximum number of files that may be used.
.IP
Input files must have at least the first 3 columns of the BED specification.
The program accepts BED and Starch file formats.
May use '\-' for a file to indicate reading from standard input (BED format only).
.IP
Process Flags:
.HP
\fB\-\-chrom\fR <chromosome> Jump to and process data for given <chromosome> only.
.TP
\fB\-\-ec\fR
Error check input files (slower).
.TP
\fB\-\-header\fR
Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
.TP
\fB\-\-help\fR
Print this message and exit successfully.
.TP
\fB\-\-help\-\fR<operation>
Detailed help on <operation>.
An example is \fB\-\-help\-c\fR or \fB\-\-help\-complement\fR
.TP
\fB\-\-range\fR L:R
Add 'L' bp to all start coordinates and 'R' bp to end
coordinates. Either value may be + or \- to grow or
shrink regions.  With the \fB\-e\fR/\-n operations, the first
(reference) file is not padded, unlike all other files.
.TP
\fB\-\-range\fR S
Pad or shrink input file(s) coordinates symmetrically by S.
This is shorthand for: \fB\-\-range\fR \fB\-S\fR:S.
.TP
\fB\-\-version\fR
Print program information.
.IP
Operations: (choose one of)
.HP
\fB\-c\fR, \fB\-\-complement\fR [\-L] File1 [File]*
.HP
\fB\-d\fR, \fB\-\-difference\fR ReferenceFile File2 [File]*
.HP
\fB\-e\fR, \fB\-\-element\-of\fR [bp | percentage] ReferenceFile File2 [File]*
.TP
by default, \fB\-e\fR 100% is used.
\&'bedops \fB\-e\fR 1' is also popular.
.HP
\fB\-i\fR, \fB\-\-intersect\fR File1 File2 [File]*
.HP
\fB\-m\fR, \fB\-\-merge\fR File1 [File]*
.HP
\fB\-n\fR, \fB\-\-not\-element\-of\fR [bp | percentage] ReferenceFile File2 [File]*
.TP
by default, \fB\-n\fR 100% is used.
\&'bedops \fB\-n\fR 1' is also popular.
.HP
\fB\-p\fR, \fB\-\-partition\fR File1 [File]*
.HP
\fB\-s\fR, \fB\-\-symmdiff\fR File1 File2 [File]*
.HP
\fB\-u\fR, \fB\-\-everything\fR File1 [File]*
.HP
\fB\-w\fR, \fB\-\-chop\fR [bp] [\-\-stagger <nt>] [\-x] File1 [File]*
.IP
by default, \fB\-w\fR 1 is used with no staggering.
.PP
Example: bedops \fB\-\-range\fR 10 \fB\-u\fR file1.bed
.IP
NOTE: Only operations \fB\-e\fR|n|u preserve all columns (no flattening)
.SH "SEE ALSO"
The full documentation for
.B bedops
is maintained as a Texinfo manual.  If the
.B info
and
.B bedops
programs are properly installed at your site, the command
.IP
.B info bedops
.PP
should give you access to the complete manual.