Struct rust_htslib::faidx::Reader

pub struct Reader { /* private fields */ }

A Fasta reader.

Implementations

impl Reader

pub fn from_path<P: AsRef<Path>>(path: P) -> Result<Self, Error>

Create a new Reader from a path.

Arguments

• path - the path to open.

pub fn from_url(url: &Url) -> Result<Self, Error>

Create a new Reader from an URL.

Arguments

• url - the url to open

pub fn fetch_seq<N: AsRef<str>>( &self, name: N, begin: usize, end: usize ) -> Result<&[u8]>

Fetch the sequence as a byte array.

Arguments

• name - the name of the template sequence (e.g., “chr1”)
• begin - the offset within the template sequence (starting with 0)
• end - the end position to return (if smaller than begin, the behavior is undefined).

pub fn fetch_seq_string<N: AsRef<str>>( &self, name: N, begin: usize, end: usize ) -> Result<String>

Fetches the sequence and returns it as string.

Arguments

• name - the name of the template sequence (e.g., “chr1”)
• begin - the offset within the template sequence (starting with 0)
• end - the end position to return (if smaller than begin, the behavior is undefined).

pub fn n_seqs(&self) -> u64

Fetches the number of sequences in the fai index

pub fn seq_name(&self, i: i32) -> Result<String>

Fetches the i-th sequence name

Arguments

• i - index to query

pub fn fetch_seq_len<N: AsRef<str>>(&self, name: N) -> u64

Fetches the length of the given sequence name.

Arguments

• name - the name of the template sequence (e.g., “chr1”)

Trait Implementations

impl Debug for Reader

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

Formats the value using the given formatter.

impl Drop for Reader

fn drop(&mut self)

Executes the destructor for this type.