Struct ModConfig 

#[non_exhaustive]
pub struct ModConfig {
    pub base: AllowedAGCTN,
    pub is_strand_plus: bool,
    pub mod_code: ModChar,
    pub win: Vec<NonZeroU32>,
    pub mod_range: Vec<OrdPair<F32Bw0and1>>,
}

Configuration for modification generation in simulated BAM files. Also refer to SimulationConfig to see how this struct can be used, and ModConfigBuilder to see how it can be built as shown below.

Example

Configure modification for cytosines on plus strand. Here, 2Cs have probabilities randomly chosen b/w 0.4-0.8, 3Cs have probabilities b/w 0.5-0.7, 2Cs have …, 3Cs have …, … repeated forever. This can be passed as an input to a routine sometime later and applied on a given sequence.

use nanalogue_core::Error;
use nanalogue_core::simulate_mod_bam::ModConfigBuilder;

let mod_config_c = ModConfigBuilder::default()
    .base('C')
    .is_strand_plus(true)
    .mod_code("m".into())
    .win(vec![2, 3])
    .mod_range(vec![(0.4, 0.8), (0.5, 0.7)]).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.

base: AllowedAGCTN

Base that is modified (A, C, G, T, or N)

is_strand_plus: bool

Whether this is on the plus strand

mod_code: ModChar

Modification code (character or numeric)

win: Vec<NonZeroU32>

Vector of window sizes for modification density variation. e.g. if you want reads with a window of 100 bases with each modified with a probability in the range 0.4-0.6 and the next 200 modified in the range 0.1-0.2 (and this two window config repeating forever), you need to set this win array to [100, 200] and the mod range array to [[0.4, 0.6], [0.1, 0.2]] (Remembering to adjust the datatypes of the inputs suitably i.e. use NonZeroU32 etc.) NOTE: “bases” in the above description refer to bases of interest set in the base field i.e. 100 bases with base set to “T” mean 100 thymidines specifically.

mod_range: Vec<OrdPair<F32Bw0and1>>

Vector of modification density range e.g. [[0.4, 0.6], [0.1, 0.2]]. Also see description of win above.

Trait Implementations

impl Clone for ModConfig

fn clone(&self) -> ModConfig

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ModConfig

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

Formats the value using the given formatter.

impl Default for ModConfig

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for ModConfig

where ModConfig: 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 ModConfig

fn eq(&self, other: &ModConfig) -> 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 ModConfig

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 ModConfig