Struct Simulate 

pub struct Simulate {

    pub reference: ReferenceOptions,
    pub vcf: VcfOptions,
    pub bed: BedOptions,
    pub output: OutputPrefixOptions,
    pub seed: SeedOptions,
    pub coverage: f64,
    pub read_length: usize,
    pub fragment_mean: usize,
    pub fragment_stddev: usize,
    pub min_fragment_length: usize,
    pub single_end: bool,
    pub adapter_r1: String,
    pub adapter_r2: String,
    pub min_error_rate: f64,
    pub max_error_rate: f64,
    pub max_n_frac: f64,
    pub methylation_mode: Option<MethylationMode>,
    pub methylation_conversion_rate: Option<f64>,
    pub methylation_failure_rate: Option<f64>,
    pub cpg_truth_bedgraph: Option<PathBuf>,
    pub golden_bam: bool,
    pub golden_vcf: bool,
    pub simple_names: bool,
    pub compression: u8,
    pub threads: usize,
}

Simulate sequencing reads from a reference genome.

Generates paired-end or single-end FASTQ files with optional ground-truth BAM and VCF outputs for benchmarking alignment and variant calling pipelines. Variants are applied from an input VCF to construct haplotype sequences, and reads are sampled with a position-dependent Illumina error model.

Fields

reference: ReferenceOptions

vcf: VcfOptions

bed: BedOptions

output: OutputPrefixOptions

seed: SeedOptions

coverage: f64

Mean sequencing coverage depth.

read_length: usize

Length of each read in bases.

fragment_mean: usize

Mean insert size (outer distance between read pair ends).

fragment_stddev: usize

Standard deviation of the insert size distribution.

min_fragment_length: usize

Minimum fragment length in bases; sampled lengths below this are clamped up. Fragments shorter than the read length are padded with adapter sequence. Must be at least 1.

single_end: bool

Generate single-end reads instead of paired-end.

adapter_r1: String

Adapter sequence appended to read 1 when the fragment is shorter than the read length.

adapter_r2: String

Adapter sequence appended to read 2 when the fragment is shorter than the read length.

min_error_rate: f64

Minimum per-base error rate, applied at the start of reads.

max_error_rate: f64

Maximum per-base error rate, applied at the end of reads.

max_n_frac: f64

Maximum fraction of a read’s bases that may come from ambiguous reference positions (IUPAC codes or N). Reference bases resolved from ambiguity codes are flagged at load time and counted per read; read pairs whose R1 or R2 exceeds this fraction are rejected and resampled. Setting this to 1.0 disables the filter; setting it to 0.0 requires every base to come from an unambiguous reference position. Value must be in [0.0, 1.0].

methylation_mode: Option<MethylationMode>

Enable methylation chemistry simulation. em-seq (or bisulfite) converts unmethylated cytosines to thymine and preserves methylated ones (matches both bisulfite and em-seq protocols). taps is the inverse: methylated cytosines convert to thymine while unmethylated ones are preserved. When omitted, no methylation chemistry is applied. Requires a methylation-annotated VCF (MT/MB FORMAT fields) produced by holodeck methylate.

methylation_conversion_rate: Option<f64>

Probability that the converting class of cytosines (unmethylated for em-seq/bisulfite, methylated for TAPS) is converted to thymine in a molecule that converted normally. 1.0 is perfect chemistry; real protocols typically achieve 0.99–0.999. Only takes effect when --methylation-mode is set; passing this flag without a mode is rejected. Defaults to 0.999 when --methylation-mode is set without this flag.

methylation_failure_rate: Option<f64>

Fraction of molecules that are whole-molecule conversion failures. Real bisulfite/EM-seq conversion is bimodal: most molecules convert near-completely, a small fraction (fragments that fail to denature or re-anneal too fast) escape conversion as a coherent unit. A failed molecule converts its should-convert cytosines at 1 - methylation-conversion-rate (near-zero), so it retains almost all of them as C across both mates. The golden BAM stamps each record with cf:i:{0|1} recording which camp the molecule was in. Only takes effect when --methylation-mode is set; passing this flag without a mode is rejected. Defaults to 0.01 (1%) when --methylation-mode is set without this flag; pass 0.0 to disable.

cpg_truth_bedgraph: Option<PathBuf>

Write a per-CpG ground-truth methylation tally in MethylDackel’s extract CpG bedGraph format. Columns: chrom start end rate (0–100) n_methylated n_unmethylated. For every reference CpG covered by at least one simulated read, counts how many reads called the site as methylated vs unmethylated according to the simulator’s per-haplotype, per-strand methylation bitmap (NOT the post-conversion sequenced base). Lets downstream evaluators measure aligner-derived methylation calls against ground truth using the same code paths that consume MethylDackel output. Requires --methylation-mode.

golden_bam: bool

Write a ground-truth BAM file with correct alignments.

golden_vcf: bool

Write a ground-truth VCF annotated with simulated coverage.

simple_names: bool

Use simple read names (holodeck::N) instead of encoding truth coordinates in the read name.

compression: u8

BGZF compression level (0-12). Lower values are faster with larger output files; higher values produce smaller files at the cost of speed. Level 0 is no compression; 1 is fastest; 12 is maximum compression.

threads: usize

Number of threads for parallel BGZF output compression.

Trait Implementations

impl Args for Simulate

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 Simulate

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

Execute the command.

impl CommandFactory for Simulate

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 Simulate

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

Formats the value using the given formatter.

impl FromArgMatches for Simulate

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 Simulate

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.