.TH SAMTOM4 "1" "July 2015" "samtom4 3ca7fe8" "User Commands"
.SH NAME
samtom4 \- Convert a SAM file generated by
.BR blasr (1)
to M4 format
.SH SYNOPSIS
.B samtom4
.I in.sam
.I reference.fasta
.I out.m4
.RI [ options ]
.SH OPTIONS
.TP
.I in.sam
Input SAM file, which is produced by blasr.
.TP
.I reference.fasta
Reference used to generate \fIfile.sam\fR.
.TP
.I out.m4
Output in
.BR blasr (1)
M4 format.
.TP
.B \-header
Print M4 header.
.TP
.B \-useShortRefName
Use abbreviated reference names obtained from \fIfile.sam\fR instead
of using full names from \fIreference.fasta\fR.
.SH SEE ALSO
.BR blasr (1)
.BR loadPulses (1)
.BR pls2fasta (1)
.BR samFilter (1)
.BR samtoh5 (1)
.BR sawriter (1)
.BR sdpMatcher (1)
.BR toAfg (1)