'\" t
.\"     Title: reapr-stats
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "REAPR\-STATS" "1" "" "\ \&" "\ \&"
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.SH "NAME"
reapr-stats \- generate REAPR stats from a BAM file
.SH "SYNOPSIS"
.sp
\fBreapr stats\fP [options] <preprocess\-output\-directory> <outprefix>
.SH "OPTIONS"
.sp
\fB\-f\fP <int>
.RS 4
Insert size [ave from stats.txt]
.RE
.sp
\fB\-i\fP <int>
.RS 4
Minimum insert size [pc1 from stats.txt]
.RE
.sp
\fB\-j\fP <int>
.RS 4
Maximum insert size [pc99 from stats.txt]
.RE
.sp
\fB\-m\fP <int>
.RS 4
Maximum read length (this doesn\(cqt need to be exact, it just
determines memory allocation, so must be >= max read length) [2000]
.RE
.sp
\fB\-p\fP <string>
.RS 4
Name of .gz perfect mapping file made by \fBperfectmap\fP
.RE
.sp
\fB\-q\fP <int>
.RS 4
Ignore reads with mapping quality less than this [0]
.RE
.sp
\fB\-s\fP <int>
.RS 4
Calculate FCD error every n\-th base
[ceil((fragment size) / 1000)]
.RE
.sp
\fB\-u\fP <string>
.RS 4
File containing list of chromosomes to look at
(one per line)
.RE
.SH "SEE ALSO"
.sp
reapr(1)