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.