NAME

       mason_methylation - Methylation Level Simulation

SYNOPSIS

       mason_methylation [OPTIONS] -i IN.fa -o OUT.fa

DESCRIPTION

       Simulate methylation levels for IN.fa and write them to OUT.fa.

OPTIONS

       -h, --help
              Display the help message.

       --version
              Display version information.

       -q, --quiet
              Low verbosity.

       -v, --verbose
              Higher verbosity.

       -vv, --very-verbose
              Highest verbosity.

       --seed INTEGER
              Seed for RNG. Default: 0.

       -i, --in INPUT_FILE
              Input  FASTA  file  with  genome.  Valid  filetypes  are:  .sam[.*], .raw[.*], .gbk[.*], .frn[.*],
              .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where
              * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

       -o, --out INPUT_FILE
              Input  FASTA  file  with  genome.  Valid  filetypes  are:  .sam[.*],  .raw[.*], .frn[.*], .fq[.*],
              .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], and .bam, where *  is  any  of  the
              following extensions: gz, bz2, and bgzf for transparent (de)compression.

   Methylation Level Simulation:
       --methylation-levels
              Enable methylation level simulation.

       --meth-cg-mu DOUBLE
              Median of beta distribution for methylation level of CpG loci. In range [0..1]. Default: 0.6.

       --meth-cg-sigma DOUBLE
              Standard  deviation  of  beta  distribution  for  methylation  level of CpG loci. In range [0..1].
              Default: 0.03.

       --meth-chg-mu DOUBLE
              Median of beta distribution for methylation level of CHG loci. In range [0..1]. Default: 0.08.

       --meth-chg-sigma DOUBLE
              Standard deviation of beta distribution for methylation  level  of  CHG  loci.  In  range  [0..1].
              Default: 0.008.

       --meth-chh-mu DOUBLE
              Median of beta distribution for methylation level of CHH loci. In range [0..1]. Default: 0.05.

       --meth-chh-sigma DOUBLE
              Standard  deviation  of  beta  distribution  for  methylation  level of CHH loci. In range [0..1].
              Default: 0.005.