.TH MASON_MATERIALIZER 1 "" "mason_materializer 2.0.9 [tarball]" ""
.SH NAME
mason_materializer \- VCF Materialization
.SH SYNOPSIS
\fBmason_materializer\fP [OPTIONS] \fB-ir\fP \fIIN.fa\fP \fB-iv\fP \fIIN.vcf\fP \fB-o\fP \fIOUT.fa\fP 
.SH DESCRIPTION
Apply variants from \fIIN.vcf\fP to \fIIN.fa\fP and write the results to \fIout.fa\fP.
.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
Low verbosity.
.TP
\fB-v\fP, \fB--verbose\fP
Higher verbosity.
.TP
\fB-vv\fP, \fB--very-verbose\fP
Highest verbosity.
.TP
\fB--seed\fP \fIINTEGER\fP
Seed for random number generation. Default: \fI0\fP.
.TP
\fB--meth-seed\fP \fIINTEGER\fP
Seed for methylation simulation random number generation. Default: \fI0\fP.
.TP
\fB-o\fP, \fB--out\fP \fIOUTPUT_FILE\fP
Output of materialized contigs. 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.
.TP
\fB--out-breakpoints\fP \fIOUTPUT_FILE\fP
TSV file to write breakpoints in variants to. Valid filetypes are: \fI.txt\fP and \fI.tsv\fP.
.TP
\fB--haplotype-name-sep\fP \fISTRING\fP
String separating contig name from haplotype number. Default: \fI/\fP.
.TP
\fB--meth-fasta-in\fP \fIINPUT_FILE\fP
FASTA file with methylation levels of the input file. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\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, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.TP
\fB--meth-fasta-out\fP \fIOUTPUT_FILE\fP
FASTA file with methylation levels of the 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.
.SS Apply VCF Variants to Reference:
.TP
\fB-ir\fP, \fB--input-reference\fP \fIINPUT_FILE\fP
Path to FASTA file to read the reference from. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\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, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.TP
\fB-iv\fP, \fB--input-vcf\fP \fIINPUT_FILE\fP
Path to the VCF file with variants to apply. Valid filetype is: \fI.vcf[.*]\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.SS Methylation Level Simulation:
.TP
\fB--methylation-levels\fP
Enable methylation level simulation.
.TP
\fB--meth-cg-mu\fP \fIDOUBLE\fP
Median of beta distribution for methylation level of CpG loci. In range [0..1]. Default: \fI0.6\fP.
.TP
\fB--meth-cg-sigma\fP \fIDOUBLE\fP
Standard deviation of beta distribution for methylation level of CpG loci. In range [0..1]. Default: \fI0.03\fP.
.TP
\fB--meth-chg-mu\fP \fIDOUBLE\fP
Median of beta distribution for methylation level of CHG loci. In range [0..1]. Default: \fI0.08\fP.
.TP
\fB--meth-chg-sigma\fP \fIDOUBLE\fP
Standard deviation of beta distribution for methylation level of CHG loci. In range [0..1]. Default: \fI0.008\fP.
.TP
\fB--meth-chh-mu\fP \fIDOUBLE\fP
Median of beta distribution for methylation level of CHH loci. In range [0..1]. Default: \fI0.05\fP.
.TP
\fB--meth-chh-sigma\fP \fIDOUBLE\fP
Standard deviation of beta distribution for methylation level of CHH loci. In range [0..1]. Default: \fI0.005\fP.
.SH VCF VARIANT NOTES
If the option \fB--input-vcf\fP/\fB-iv\fP 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.
.sp
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 \fImason_variator\fP program are guaranteed to be read.
.sp
Only the haplotypes of the first individual will be generated.