.TH MASON_GENOME 1 "" "mason_genome 2.0.9 [tarball]" ""
.SH NAME
mason_genome \- Random Genome Simulation
.SH SYNOPSIS
\fBmason_genome\fP [\fIOPTIONS\fP] [\fB-l\fP \fILEN\fP]+ \fB-o\fP \fIOUT.fa\fP
.SH DESCRIPTION
Simulate a random genome to the output file.  For each \fB-l\fP/\fB--contig-length\fP entry, a contig with the given length will be simulated.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.TP
\fB-q\fP, \fB--quiet\fP
Set verbosity to a minimum.
.TP
\fB-v\fP, \fB--verbose\fP
Enable verbose output.
.TP
\fB-vv\fP, \fB--very-verbose\fP
Enable very verbose output.
.SS Simulation Configuration:
.TP
\fB-l\fP, \fB--contig-length\fP List of \fIINTEGER\fP's
Length of the contig to simulate. Give one \fB-l\fP value for each contig to simulate. In range [1..inf].
.TP
\fB-s\fP, \fB--seed\fP \fIINTEGER\fP
The seed to use for the random number generator. Default: \fI0\fP.
.SS Output Options:
.TP
\fB-o\fP, \fB--out-file\fP \fIOUTPUT_FILE\fP
Output file. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.SH EXAMPLES
.TP
\fBmason_genome\fP \fB-l\fP 1000 \fB-l\fP 4000 \fB-o\fP \fIgenome.fa\fP
Simulate a genome with two contigs of lengths 1000 and 4000 and write it to genome.fa.