NAME

       mason_materializer - VCF Materialization

SYNOPSIS

       mason_materializer [OPTIONS] -ir IN.fa -iv IN.vcf -o OUT.fa

DESCRIPTION

       Apply variants from IN.vcf to IN.fa and write the results 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 random number generation. Default: 0.

       --meth-seed INTEGER
              Seed for methylation simulation random number generation. Default: 0.

       -o, --out OUTPUT_FILE
              Output  of materialized contigs. 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.

       --out-breakpoints OUTPUT_FILE
              TSV file to write breakpoints in variants to. Valid filetypes are: .txt and .tsv.

       --haplotype-name-sep STRING
              String separating contig name from haplotype number. Default: /.

       --meth-fasta-in INPUT_FILE
              FASTA file with  methylation  levels  of  the  input  file.  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.

       --meth-fasta-out OUTPUT_FILE
              FASTA  file  with  methylation  levels  of  the  output  file. 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.

   Apply VCF Variants to Reference:
       -ir, --input-reference INPUT_FILE
              Path to FASTA file to read the  reference  from.  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.

       -iv, --input-vcf INPUT_FILE
              Path  to  the VCF file with variants to apply. Valid filetype is: .vcf[.*], 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.

VCF VARIANT NOTES

       If  the  option  --input-vcf/-iv is given then the given VCF file is read and the variants
       are applied to the input reference file.  If it is not given then the input reference file
       is taken verbatimly for simulating reads.

       There  are  some  restrictions  on the VCF file and the application of the variants to the
       reference will fail if the VCF file is non-conforming.  VCF files from the  mason_variator
       program are guaranteed to be read.

       Only the haplotypes of the first individual will be generated.