.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH MAF-CONVERT "1" "January 2019" "maf-convert 963" "User Commands"
.SH NAME
maf-convert \- Convert MAF-format alignments to tabular format
.SH DESCRIPTION
.SS "Usage:"
.IP
maf\-convert \fB\-\-help\fR
maf\-convert axt mafFile(s)
maf\-convert blast mafFile(s)
maf\-convert blasttab mafFile(s)
maf\-convert chain mafFile(s)
maf\-convert html mafFile(s)
maf\-convert psl mafFile(s)
maf\-convert sam mafFile(s)
maf\-convert tab mafFile(s)
.PP
Read MAF\-format alignments & write them in another format.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-p\fR, \fB\-\-protein\fR
assume protein alignments, for psl match counts
.TP
\fB\-j\fR N, \fB\-\-join\fR=\fI\,N\/\fR
join co\-linear alignments separated by <= N letters
.TP
\fB\-n\fR, \fB\-\-noheader\fR
omit any header lines from the output
.TP
\fB\-d\fR, \fB\-\-dictionary\fR
include dictionary of sequence lengths in sam format
.TP
\fB\-f\fR DICTFILE, \fB\-\-dictfile\fR=\fI\,DICTFILE\/\fR
get sequence dictionary from DICTFILE
.TP
\fB\-r\fR READGROUP, \fB\-\-readgroup\fR=\fI\,READGROUP\/\fR
read group info for sam format
.TP
\fB\-l\fR LINESIZE, \fB\-\-linesize\fR=\fI\,LINESIZE\/\fR
line length for blast and html formats (default: 60)