Struct gfatk::gfa::gfa::GFAtk

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pub struct GFAtk(pub GFA<usize, OptionalFields>);

Expand description

A wrapper around GFA from the gfa crate

Tuple Fields

0: GFA<usize, OptionalFields>

Implementations

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impl GFAtk

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pub fn into_ungraph(&self) -> Result<(GFAGraphLookups, GFAungraph )>

Returns a tuple of GFAGraphLookups (a struct of indices/node names) and an undirected GFA graph structure.

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pub fn into_digraph(&self) -> Result<(GFAGraphLookups, GFAdigraph )>

Returns a tuple of GFAGraphLookups (a struct of indices/node names) and an directed GFA graph structure.

Most functionality of this binary is on directed graph structures

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pub fn print_extract(&self, sequences_to_keep: Vec<usize>)

A method to print a GFA to STDOUT, given a vector of sequence ID’s to keep.

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pub fn make_overlaps(&self, extend_length: usize) -> Result<Overlaps>

Returns the overlaps between all the segments in a GFA.

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pub fn print_sequences(
&self,
subgraph_index_header: Option<String>
) -> Result<()>

The internal function called when gfatk fasta is called.

Prints all segments of the GFA as-is.

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fn parse_coverage_opt(opt: &OptFieldVal) -> Result<&f32>

Two internal functions below to parse coverage of a GFA segment.

Used in gfatk stats.

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fn get_coverage(&self) -> Result<f32>

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pub fn node_seq_len_and_cov(&self, node: usize) -> Result<(usize, f32 )>

Return the coverage and sequence length for a segment, given a segment name.

Note segment names are always usize.

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pub fn sequence_stats(
 &self,
 genome_type: GenomeType,
 tabular: bool
) -> Result<(f32, f32, usize )>

The internal function called in gfatk stats.

Returns average GC%, average coverage, and total sequence length for a GFA (sub)graph.

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pub fn gen_cov_hash(
&self,
graph_lookup: &GFAGraphLookups
) -> Result<HashMap<NodeIndex, usize>>

Returns a HashMap of relative coverage of each node (segment) in the GFA.

Relative here indicates that each segment coverage is divided by the lowest coverage node, and rounded.

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pub fn from_path_cli(
 &self,
 path: GFAPath,
 link_map: HashMap<String, usize>,
 call: &str,
 fasta_header: Option<&str>
) -> Result<()>

Take a GFAPath and print out the path from a GFA.

Currently implemented requires two loops of the GFA, and storage of the sequences in a HashMap.

Trait Implementations

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impl Clone for GFAtk

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fn clone(&self) -> GFAtk

Returns a copy of the value. Read more

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

Performs copy-assignment from source. Read more

Auto Trait Implementations

impl RefUnwindSafe for GFAtk

impl Send for GFAtk

impl Sync for GFAtk

impl Unpin for GFAtk

impl UnwindSafe for GFAtk

Blanket Implementations

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impl<T> Any for T where
T: 'static + ?Sized,

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fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

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impl<T> Borrow<T> for T where
T: ?Sized,

const: unstable · source

fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

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impl<T> BorrowMut<T> for T where
T: ?Sized,

const: unstable · source

fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more

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impl<T> From<T> for T

const: unstable · source

fn from(t: T) -> T

Returns the argument unchanged.

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impl<T, U> Into for T where
U: From<T>,

const: unstable · source

fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

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impl<T> ToOwned for T where
T: Clone,

type Owned = T

The resulting type after obtaining ownership.

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fn to_owned(&self) -> T

Creates owned data from borrowed data, usually by cloning. Read more

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fn clone_into(&self, target: &mut T)

🔬 This is a nightly-only experimental API. (toowned_clone_into)

Uses borrowed data to replace owned data, usually by cloning. Read more

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impl<T, U> TryFrom for T where
U: Into<T>,

type Error = Infallible

The type returned in the event of a conversion error.

const: unstable · source

fn try_from(value: U) -> Result<T, <T as TryFrom>::Error>

Performs the conversion.

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impl<T, U> TryInto for T where
U: TryFrom<T>,

type Error = >::Error

The type returned in the event of a conversion error.

const: unstable · source

fn try_into(self) -> Result<U, >::Error>

Performs the conversion.

Struct gfatk::gfa::gfa::GFAtk

Tuple Fields

Implementations

impl GFAtk

pub fn into_ungraph(&self) -> Result<(GFAGraphLookups, GFAungraph)>

pub fn into_digraph(&self) -> Result<(GFAGraphLookups, GFAdigraph)>

pub fn print_extract(&self, sequences_to_keep: Vec<usize>)

pub fn make_overlaps(&self, extend_length: usize) -> Result<Overlaps>

pub fn print_sequences( &self, subgraph_index_header: Option<String>) -> Result<()>

fn parse_coverage_opt(opt: &OptFieldVal) -> Result<&f32>

fn get_coverage(&self) -> Result<f32>

pub fn node_seq_len_and_cov(&self, node: usize) -> Result<(usize, f32)>

pub fn sequence_stats( &self, genome_type: GenomeType, tabular: bool) -> Result<(f32, f32, usize)>

pub fn gen_cov_hash( &self, graph_lookup: &GFAGraphLookups) -> Result<HashMap<NodeIndex, usize>>

pub fn from_path_cli( &self, path: GFAPath, link_map: HashMap<String, usize>, call: &str, fasta_header: Option<&str>) -> Result<()>

Trait Implementations

impl Clone for GFAtk

fn clone(&self) -> GFAtk

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

Auto Trait Implementations

impl RefUnwindSafe for GFAtk

impl Send for GFAtk

impl Sync for GFAtk

impl Unpin for GFAtk

impl UnwindSafe for GFAtk

Blanket Implementations

impl<T> Any for T where T: 'static + ?Sized,

fn type_id(&self) -> TypeId

impl<T> Borrow<T> for T where T: ?Sized,

fn borrow(&self) -> &T

impl<T> BorrowMut<T> for T where T: ?Sized,

fn borrow_mut(&mut self) -> &mut T

impl<T> From<T> for T

fn from(t: T) -> T

impl<T, U> Into<U> for T where U: From<T>,

fn into(self) -> U

impl<T> ToOwned for T where T: Clone,

type Owned = T

fn to_owned(&self) -> T

fn clone_into(&self, target: &mut T)

impl<T, U> TryFrom<U> for T where U: Into<T>,

type Error = Infallible

fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

impl<T, U> TryInto<U> for T where U: TryFrom<T>,

type Error = <U as TryFrom<T>>::Error

fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

pub fn into_ungraph(&self) -> Result<(GFAGraphLookups, GFAungraph )>

pub fn into_digraph(&self) -> Result<(GFAGraphLookups, GFAdigraph )>

pub fn print_sequences(
&self,
subgraph_index_header: Option<String>
) -> Result<()>

pub fn node_seq_len_and_cov(&self, node: usize) -> Result<(usize, f32 )>

pub fn sequence_stats(
&self,
genome_type: GenomeType,
tabular: bool
) -> Result<(f32, f32, usize )>

pub fn gen_cov_hash(
&self,
graph_lookup: &GFAGraphLookups
) -> Result<HashMap<NodeIndex, usize>>

pub fn from_path_cli(
&self,
path: GFAPath,
link_map: HashMap<String, usize>,
call: &str,
fasta_header: Option<&str>
) -> Result<()>

impl<T> Any for T where
T: 'static + ?Sized,

impl<T> Borrow<T> for T where
T: ?Sized,

impl<T> BorrowMut<T> for T where
T: ?Sized,

impl<T, U> Into<U> for T where
U: From<T>,

impl<T> ToOwned for T where
T: Clone,

impl<T, U> TryFrom<U> for T where
U: Into<T>,

impl<T, U> TryInto<U> for T where
U: TryFrom<T>,