Struct SubgraphQuery 

pub struct SubgraphQuery { /* private fields */ }

Arguments for extracting a subgraph.

Examples

use gbz_base::SubgraphQuery;
use gbz::FullPathName;

let path_name = FullPathName::generic("path");
let query = SubgraphQuery::path_offset(&path_name, 123);
assert_eq!(query.context(), SubgraphQuery::DEFAULT_CONTEXT);
assert_eq!(query.snarls(), SubgraphQuery::DEFAULT_SNARLS);
assert_eq!(query.output(), SubgraphQuery::DEFAULT_OUTPUT);

let query = query.with_context(1000);
assert_eq!(query.context(), 1000);

let query = query.with_snarls(true);
assert!(query.snarls());

Implementations

impl SubgraphQuery

pub const DEFAULT_CONTEXT: usize = 100

Default value for context length (in bp).

pub const DEFAULT_SNARLS: bool = false

Default value for the snarl extraction flag.

pub const DEFAULT_OUTPUT: HaplotypeOutput = HaplotypeOutput::All

Default value for the haplotype output option.

pub fn path_offset(path_name: &FullPathName, offset: usize) -> Self

Creates a query that retrieves a subgraph around a path offset.

The reference path should be specified by using a sample name, a contig name, and optionally a haplotype number. The fragment field should not be used. If the reference haplotype is fragmented, the query will try to find the right fragment.

pub fn path_interval(path_name: &FullPathName, interval: Range<usize>) -> Self

Cretes a query that retrieves a subgraph around a path interval.

The reference path should be specified by using a sample name, a contig name, and optionally a haplotype number. The fragment field should not be used. If the reference haplotype is fragmented, the query will try to find the right fragment.

pub fn nodes(nodes: impl IntoIterator<Item = usize>) -> Self

Creates a query that retrieves a subgraph around a set of nodes.

pub fn between(start: usize, end: usize, limit: Option<usize>) -> Self

Creates a query that extracts a subgraph between two handles in the same chain.

This query ignores context length and the snarl extraction flag. An optional safety limit for the size of the subgraph in nodes can be provided. If the nodes are not in the same chain in the given order, the subgraph can otherwise be arbitrarily large.

pub fn with_context(self, context: usize) -> Self

Returns an updated query with the given context length.

See Self::DEFAULT_CONTEXT for the default value.

pub fn with_snarls(self, snarls: bool) -> Self

Returns an updated query with the given snarl extraction flag.

See Self::DEFAULT_SNARLS for the default value.

pub fn with_output(self, output: HaplotypeOutput) -> Self

Returns an updated query with the given haplotype output option.

See Self::DEFAULT_OUTPUT for the default value.

Panics

Panics if this is a node-based query and the output would be HaplotypeOutput::ReferenceOnly.

pub fn context(&self) -> usize

Returns the context length (in bp) for the query.

pub fn snarls(&self) -> bool

Returns true if the query also extracts nodes coverered top-level snarls.

A snarl is covered, if both of its boundary nodes are contained in the query interval or in the context.

pub fn output(&self) -> HaplotypeOutput

Returns the output format for the query.

Trait Implementations

impl Clone for SubgraphQuery

fn clone(&self) -> SubgraphQuery

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for SubgraphQuery

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

Formats the value using the given formatter.

impl Display for SubgraphQuery

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

Formats the value using the given formatter.

impl PartialEq for SubgraphQuery

fn eq(&self, other: &SubgraphQuery) -> 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 Eq for SubgraphQuery

impl StructuralPartialEq for SubgraphQuery