'\" t
.\"     Title: reapr-pipeline
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "REAPR\-PIPELINE" "1" "" "\ \&" "\ \&"
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.SH "NAME"
reapr-pipeline \- run the REAPR pipeline
.SH "SYNOPSIS"
.sp
\fBreapr pipeline\fP [options] <assembly.fa> <in.bam> <outdirectory> [perfectmapprefix]
.SH "DESCRIPTION"
.sp
[perfectmapprefix] is optional and should be the prefix used when task
\fBperfectmap\fP was run.
.sp
It is assumed that reads in <in.bam> are \*(Aqinnies\*(Aq, i.e. the correct orientation
is reads in a pair pointing towards each other (\-\-\(-> \(<-\-\-).
.SH "OPTIONS"
.sp
\fB\-stats|fcdrate|score|break option=value\fP
.RS 4
You can pass options to \fBstats\fP, \fBfcdrate\fP, \fBscore\fP or \fBbreak\fP
if you want to change the default settings. These
can be used multiple times to use more than one option. e.g.:
\fB\-stats i=100 \-stats j=1000\fP
If an option has no value, use \fB1\fP. e.g.
\fB\-break b=1\fP
.RE
.sp
\fB\-fcdcut\fP <float>
.RS 4
Set the fcdcutoff used when running score. Default is to
run fcdrate to determine the cutoff. Using this option will
skip fcdrate and use the given value.
.RE
.sp
\fB\-x\fP
.RS 4
By default, a bash script is written to run all
the pipeline stages. Using this option stops the
script from being run.
.RE
.SH "SEE ALSO"
.sp
reapr(1)