.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH PROPMAPPED "1" "February 2020" "propmapped 2.0.0+dfsg-1~bpo10+1" "User Commands"
.SH NAME
propmapped \- calculate the proportion of mapped reads/fragments
.SH USAGE
.PP
prommapped [options] \fB\-i\fR <file>
.PP
Required arguments:
.TP
\fB\-i\fR <string>
An input file containing read mapping results. Both SAM or BAM
formats are supported.
.PP
Optional arguments:
.TP
\fB\-o\fR <string>
Name of output file including mapping statistics.
.TP
\fB\-f\fR
If specified, fragments (read pairs) will be counted instead of
individual reads. This option is only applicable for paired\-end
reads.
.TP
\fB\-p\fR
If specified, only properly paired reads will be counted. This
option is only applicable for paired\-end reads.
.PP
propMapped v2.0.0
.IP
Calculate the proportion of mapped reads/fragments.
.PP