.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH REPAIR "1" "June 2017" "repair 1.5.1+dfsg-4~bpo8+1" "User Commands"
.SH NAME
repair \- a component of subread suite
.SH USAGE

\fBrepair\fR [options] \fB\-i\fR <input_file> \fB\-o\fR <output_file>
.PP
Required arguments:
.TP
\fB\-i\fR <string>
Name of input file. BAM format by default.
.TP
\fB\-o\fR <string>
Name of output file. The output file is in BAM format.
.PP
Optional arguments:
.TP
\fB\-S\fR
The input file is in SAM format.
.TP
\fB\-c\fR
Compress the output BAM file. This will reduce the size of BAM
file, but will increase the time of retrieving reads from BAM
file.
.TP
\fB\-T\fR <int>
Number of CPU threads. 8 by default.
.TP
\fB\-d\fR
Do not add dummy reads for singleton reads.
.TP
\fB\-t\fR
Do not include sequences and quality scores of reads in the
output file.