Struct Methylate 

pub struct Methylate {
    pub reference: ReferenceOptions,
    pub vcf: VcfOptions,
    pub seed: SeedOptions,
    pub methylation_rate_island: f64,
    pub methylation_rate_shore: f64,
    pub methylation_rate_open_sea: f64,
    pub methylation_correlation_length_island: f64,
    pub methylation_correlation_length_shore: f64,
    pub methylation_correlation_length_open_sea: f64,
    pub hemimethylation_rate: f64,
    pub output: PathBuf,
    pub bedgraph: Option<PathBuf>,
}

Generate a methylation-annotated VCF.

Scans every CpG dinucleotide in the reference (optionally after applying variants from a VCF) and records per-haplotype, per-strand methylation state for each site. Methylation is assigned with a context-aware Markov model: CpGs are classified into island / shore / open-sea (detected de novo from the sequence), each with its own target rate and spatial correlation length, so islands come out hypomethylated, open-sea hypermethylated, with autocorrelated runs in between. Methylation is symmetric by default with a low sporadic hemimethylation rate. Per-haplotype draws give allele-specific methylation. All draws are deterministic from --seed.

Fields

reference: ReferenceOptions

vcf: VcfOptions

seed: SeedOptions

methylation_rate_island: f64

Target methylation fraction for CpG-island-interior CpGs. Islands are characteristically hypomethylated, so this defaults low. Must be in [0.0, 1.0]. To methylate uniformly (no island structure), set the three context rates equal.

methylation_rate_shore: f64

Target methylation fraction for island-shore CpGs (within 2 kb of an island; intermediate methylation). Must be in [0.0, 1.0].

methylation_rate_open_sea: f64

Target methylation fraction for open-sea CpGs (the hypermethylated bulk of the genome, away from islands). Must be in [0.0, 1.0].

methylation_correlation_length_island: f64

Spatial correlation length (bp) for island-interior CpGs: larger values give longer runs of like-methylated CpGs. Must be > 0.

methylation_correlation_length_shore: f64

Spatial correlation length (bp) for shore CpGs. Must be > 0.

methylation_correlation_length_open_sea: f64

Spatial correlation length (bp) for open-sea CpGs. Must be > 0.

hemimethylation_rate: f64

Probability that a methylated CpG is made hemimethylated — exactly one strand left unmethylated. Real hemimethylation is sporadic and rare, so this defaults low. Must be in [0.0, 1.0].

output: PathBuf

Output methylation-annotated VCF (BGZF-compressed).

bedgraph: Option<PathBuf>

Optional MethylDackel-format population-fraction bedGraph derived closed-form from the genome model. Independent of any read coverage.

Trait Implementations

impl Args for Methylate

fn group_id() -> Option<Id>

Report the ArgGroup::id for this set of arguments

fn augment_args<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate Self via FromArgMatches::from_arg_matches_mut

fn augment_args_for_update<'b>(__clap_app: Command) -> Command

Append to Command so it can instantiate self via FromArgMatches::update_from_arg_matches_mut

impl Command for Methylate

fn execute(&self) -> Result<()>

Execute the command.

impl CommandFactory for Methylate

fn command<'b>() -> Command

Build a Command that can instantiate Self.

fn command_for_update<'b>() -> Command

Build a Command that can update self.

impl Debug for Methylate

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl FromArgMatches for Methylate

fn from_arg_matches(__clap_arg_matches: &ArgMatches) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn from_arg_matches_mut( __clap_arg_matches: &mut ArgMatches, ) -> Result<Self, Error>

Instantiate Self from ArgMatches, parsing the arguments as needed.

fn update_from_arg_matches( &mut self, __clap_arg_matches: &ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

fn update_from_arg_matches_mut( &mut self, __clap_arg_matches: &mut ArgMatches, ) -> Result<(), Error>

Assign values from ArgMatches to self.

impl Parser for Methylate

fn parse() -> Self

Parse from std::env::args_os(), exit on error.

fn try_parse() -> Result<Self, Error>

Parse from std::env::args_os(), return Err on error.

fn parse_from<I, T>(itr: I) -> Self

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, exit on error.

fn try_parse_from<I, T>(itr: I) -> Result<Self, Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Parse from iterator, return Err on error.

fn update_from<I, T>(&mut self, itr: I)

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, exit on error.

fn try_update_from<I, T>(&mut self, itr: I) -> Result<(), Error>

where I: IntoIterator<Item = T>, T: Into<OsString> + Clone,

Update from iterator, return Err on error.