.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH ABYSS-FIXMATE "1" "December 2020" "ABySS 2.2.5" "User Commands"
.SH NAME
abyss-fixmate \- Fill the paired-end fields of SAM alignments
.SH SYNOPSIS
.B abyss-fixmate
[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
.SH DESCRIPTION
Write read pairs that map to the same contig to the file SAME.
Write read pairs that map to different contigs to stdout.
Alignments may be in FILE(s) or standard input.
.IP
Options:
.TP
\fB\-\-no\-qname\fR
set the qname to * [default]
.TP
\fB\-\-qname\fR
do not alter the qname
.TP
\fB\-\-all\fR
print all alignments
.TP
\fB\-\-diff\fR
print alignments that align to different
contigs [default]
.TP
\fB\-l\fR, \fB\-\-min\-align\fR=\fI\,N\/\fR
the minimal alignment size [1]
.TP
\fB\-s\fR, \fB\-\-same\fR=\fI\,SAME\/\fR
write properly\-paired reads to this file
.TP
\fB\-h\fR, \fB\-\-hist\fR=\fI\,FILE\/\fR
write the fragment size histogram to FILE
.TP
\fB\-c\fR, \fB\-\-cov\fR=\fI\,FILE\/\fR
write the physical coverage to FILE
.TP
\fB\-v\fR, \fB\-\-verbose\fR
display verbose output
.TP
\fB\-\-help\fR
display this help and exit
.TP
\fB\-\-version\fR
output version information and exit
.TP
\fB\-\-db\fR=\fI\,FILE\/\fR
specify path of database repository in FILE
.TP
\fB\-\-library\fR=\fI\,NAME\/\fR
specify library NAME for sqlite
.TP
\fB\-\-strain\fR=\fI\,NAME\/\fR
specify strain NAME for sqlite
.TP
\fB\-\-species\fR=\fI\,NAME\/\fR
specify species NAME for sqlite
.SH AUTHOR
Written by Shaun Jackman.
.SH "REPORTING BUGS"
Report bugs to <abyss\-users@bcgsc.ca>.
.SH COPYRIGHT
Copyright 2014 Canada's Michael Smith Genome Sciences Centre