Struct SimulationConfig 

#[non_exhaustive]
pub struct SimulationConfig {
    pub contigs: ContigConfig,
    pub reads: Vec<ReadConfig>,
}

Main configuration struct for simulation.

After construction, you can pass it to crate::simulate_mod_bam::run to create a mod BAM file. You can build this using SimulationConfigBuilder as shown below.

Example

Below struct can be used in appropriate routines to create a BAM file.

use nanalogue_core::Error;
use nanalogue_core::simulate_mod_bam::{ContigConfigBuilder, SimulationConfigBuilder,
    ReadConfigBuilder, ModConfigBuilder};

// Request two contigs with lengths randomly chosen from 1000 - 2000 bp.
let contig_config = ContigConfigBuilder::default()
    .number(2)
    .len_range((1000,2000)).build()?;

// First set of reads
let read_config1 = ReadConfigBuilder::default()
    .number(100)
    .mapq_range((10, 20))
    .base_qual_range((30, 40))
    .len_range((0.5, 0.6));

// second set of reads, now 200 requested with a modification and a barcode
let mod_config = ModConfigBuilder::default()
    .base('C')
    .is_strand_plus(true)
    .mod_code("m".into())
    .win(vec![2, 3])
    .mod_range(vec![(0.1, 0.8), (0.3, 0.4)]).build()?;

let read_config2 = read_config1.clone()
    .number(200)
    .barcode("AATTG".into())
    .mods(vec![mod_config]);

// set simulation config, ready to be fed into an appropriate function
let sim_config = SimulationConfigBuilder::default()
    .contigs(contig_config)
    .reads(vec![read_config1.build()?, read_config2.build()?]).build()?;

Fields (Non-exhaustive)

Non-exhaustive structs could have additional fields added in future. Therefore, non-exhaustive structs cannot be constructed in external crates using the traditional Struct { .. } syntax; cannot be matched against without a wildcard ..; and struct update syntax will not work.

contigs: ContigConfig

Configuration for contig generation

reads: Vec<ReadConfig>

Configuration for read generation

Trait Implementations

impl Clone for SimulationConfig

fn clone(&self) -> SimulationConfig

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for SimulationConfig

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

Formats the value using the given formatter.

impl Default for SimulationConfig

fn default() -> SimulationConfig

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for SimulationConfig

where SimulationConfig: Default,

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl PartialEq for SimulationConfig

fn eq(&self, other: &SimulationConfig) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Serialize for SimulationConfig

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl StructuralPartialEq for SimulationConfig