Struct SimulateArgs 

pub struct SimulateArgs {

    pub ref_fasta: String,
    pub gtf: String,
    pub out_prefixes: Vec<String>,
    pub chrom: Option<String>,
    pub circ_count: usize,
    pub switching_event: usize,
    pub circ_coverage: f64,
    pub linear_coverage: f64,
    pub scale: f64,
    pub read_len: usize,
    pub insert_len: usize,
    pub insert_sd: f64,
    pub insert_len_minor: usize,
    pub insert_sd_minor: f64,
    pub minor_insert_fraction: f64,
    pub error_rate: f64,
    pub exon_exclusive_rate: f64,
    pub seed: u64,
}

Command-line options for the standalone simulator.

Defaults approximate a compact PE150 RNA-seq fixture. The circular and linear abundance knobs are coverage means; sampled values are converted into paired-end read-pair counts by the fixed formulas in the design document.

Fields

ref_fasta: String

Reference genome FASTA.

gtf: String

Source GTF annotation used to choose circular and linear transcript exon chains.

out_prefixes: Vec<String>

Output prefix; pass two prefixes to generate a matched switching pair.

chrom: Option<String>

Optional chromosome filter, for example chr1.

circ_count: usize

Number of circular RNA loci to simulate.

switching_event: usize

Number of two-isoform circRNAs whose major isoform switches between two samples.

circ_coverage: f64

Mean circRNA coverage; per-circ coverage is sampled with --scale.

linear_coverage: f64

Mean linear transcript coverage used to size the background read set.

scale: f64

Relative standard deviation for Gaussian coverage sampling.

read_len: usize

Read length for ordinary paired-end reads.

insert_len: usize

Mean fragment span in transcript/circular coordinates.

insert_sd: f64

Standard deviation of the primary fragment span distribution.

insert_len_minor: usize

Mean fragment span for the minor long-fragment distribution.

insert_sd_minor: f64

Standard deviation of the minor long-fragment distribution.

minor_insert_fraction: f64

Fraction of fragments sampled from the minor long-fragment distribution.

error_rate: f64

Per-base substitution probability for ordinary reads.

exon_exclusive_rate: f64

Per-unique-exon probability of marking an exon coordinate circRNA-exclusive.

seed: u64

Deterministic seed controlling annotation sampling, isoforms and reads.

Trait Implementations

impl Args for SimulateArgs

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 Clone for SimulateArgs

fn clone(&self) -> SimulateArgs

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl CommandFactory for SimulateArgs

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 SimulateArgs

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

Formats the value using the given formatter.

impl FromArgMatches for SimulateArgs

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 SimulateArgs

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.