'\" t
.\"     Title: reapr-score
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "REAPR\-SCORE" "1" "" "\ \&" "\ \&"
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.SH "NAME"
reapr-score \- calculate scores and assembly errors
.SH "SYNOPSIS"
.sp
\fBreapr score\fP [options] <assembly.fa.gaps.gz> <in.bam> <statsprefix> <FCDcutoff> <outprefix>
.SH "OPTIONS"
.sp
\fB\-f\fP <int>
.RS 4
Minimum inner fragment coverage [1]
.RE
.sp
\fB\-g\fP <int>
.RS 4
Max gap length to call over [0.5 * outer_mean_insert_size]
.RE
.sp
\fB\-l\fP <int>
.RS 4
Length of window [100]
.RE
.sp
\fB\-p\fP <int>
.RS 4
Use perfect mapping reads score with given min coverage.
Incompatible with \-P.
.RE
.sp
\fB\-P\fP <int>
.RS 4
Same as \-p, but force the score to be zero at any position with
at least the given coverage of perfect mapping reads and which has an
OK insert plot, , i.e. perfect mapping reads + insert distribution
override all other tests when calculating the score.
Incompatible with \-p.
.RE
.sp
\fB\-q\fP <float>
.RS 4
Max bad read ratio [0.33]
.RE
.sp
\fB\-r\fP <int>
.RS 4
Min read coverage [max(1, mean_read_cov \- 4 * read_cov_stddev)]
.RE
.sp
\fB\-R\fP <int>
.RS 4
Repeat calling cutoff. \-R N means call a repeat if fragment
coverage is >= N times (expected coverage).
Use \-R 0 to not call repeats [2]
.RE
.sp
\fB\-s\fP <int>
.RS 4
Min score to report in errors file [0.4]
.RE
.sp
\fB\-u\fP <int>
.RS 4
FCD error window length for error calling [insert_size / 2]
.RE
.sp
\fB\-w\fP <float>
.RS 4
Min percentage of bases in window needed to call as bad [0.8]
.RE
.SH "SEE ALSO"
.sp
reapr(1)