Struct bed_reader::MetadataBuilder

pub struct MetadataBuilder { /* private fields */ }

Builder for Metadata.

Implementations

impl MetadataBuilder

pub fn build(&self) -> Result<Metadata, BedErrorPlus>

Create Metadata from the builder.

See Metadata::builder()

pub fn fid<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    fid: I
) -> &mut Self

Set the family id (fid) values.

pub fn iid<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    iid: I
) -> &mut Self

Set the individual id (iid) values.

use ndarray as nd;
use bed_reader::{Metadata, assert_eq_nan};

let metadata = Metadata::builder()
   .iid(["sample1", "sample2", "sample3"])
   .build()?;
println!("{:?}", metadata.iid()); // Outputs ndarray Some(["sample1", "sample2", "sample3"])

pub fn father<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    father: I
) -> &mut Self

Set the father values.

pub fn mother<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    mother: I
) -> &mut Self

Override the mother values.

pub fn sex<I: IntoIterator<Item = i32>>(&mut self, sex: I) -> &mut Self

Override the sex values.

pub fn pheno<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    pheno: I
) -> &mut Self

Override the phenotype values.

pub fn chromosome<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    chromosome: I
) -> &mut Self

Override the chromosome values.

pub fn sid<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    sid: I
) -> &mut Self

Override the SNP id (sid) values.

use ndarray as nd;
use bed_reader::{Metadata, assert_eq_nan};

let metadata = Metadata::builder()
   .sid(["SNP1", "SNP2", "SNP3", "SNP4"])
   .build()?;
println!("{:?}", metadata.sid()); // Outputs ndarray Some(["SNP1", "SNP2", "SNP3", "SNP4"])

pub fn cm_position<I: IntoIterator<Item = f32>>(
    &mut self,
    cm_position: I
) -> &mut Self

Override the centimorgan position values.

pub fn bp_position<I: IntoIterator<Item = i32>>(
    &mut self,
    bp_position: I
) -> &mut Self

Override the base-pair position values.

pub fn allele_1<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    allele_1: I
) -> &mut Self

Override the allele 1 values.

pub fn allele_2<I: IntoIterator<Item = T>, T: AsRef<str>>(
    &mut self,
    allele_2: I
) -> &mut Self

Override the allele 2 values.

pub fn metadata(&mut self, metadata: &Metadata) -> &mut Self

Merge metadata from a Metadata.

Example

In the example, we create a Metadata with iid and sid arrays. Next, we use another MetadataBuilder to set an fid array and an iid array. Then, we add the first Metadata to the MetadataBuilder, overwriting iid and setting sid. Finally, we print these three arrays and chromosome. Chromosome is None.

 use ndarray as nd;
 use bed_reader::Metadata;

 let metadata1 = Metadata::builder()
     .iid(["i1", "i2", "i3"])
     .sid(["s1", "s2", "s3", "s4"])
     .build()?;
 let metadata2 = Metadata::builder()
     .fid(["f1", "f2", "f3"])
     .iid(["x1", "x2", "x3"])
     .metadata(&metadata1)
     .build()?;

 println!("{0:?}", metadata2.fid()); // Outputs optional ndarray Some(["f1", "f2", "f3"]...)
 println!("{0:?}", metadata2.iid()); // Outputs optional ndarray Some(["i1", "i2", "i3"]...)
 println!("{0:?}", metadata2.sid()); // Outputs optional ndarray Some(["s1", "s2", "s3", "s4"]...)
 println!("{0:?}", metadata2.chromosome()); // Outputs None

Trait Implementations

impl Clone for MetadataBuilder

fn clone(&self) -> MetadataBuilder

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Default for MetadataBuilder

fn default() -> Self

Returns the “default value” for a type.