Struct Reader

Source

pub struct Reader { /* private fields */ }

Expand description

A Fasta reader.

Implementations§

Source §

impl Reader

Source

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.

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

Create a new Reader from an URL.

§Arguments

url - the url to open

Source

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).

Source

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).

Source

pub fn n_seqs(&self) -> u64

Fetches the number of sequences in the fai index

Source

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

Fetches the i-th sequence name

§Arguments

i - index to query

Source

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”)

Source

pub fn seq_names(&self) -> Result<Vec<String>>

Returns a Result<Vector> for all seq names.

§Errors

errors::Error::FaidxBadSeqName - missing sequence name for sequence id.

If thrown, the index is malformed, and the number of sequences in the index does not match the number of sequence names available.

 use rust_htslib::faidx::build;
 let path = std::path::PathBuf::from(concat!(env!("CARGO_MANIFEST_DIR"),"/test/test_cram.fa"));
 build(&path).expect("Failed to build fasta index");
 let reader = rust_htslib::faidx::Reader::from_path(path).expect("Failed to open faidx");
 assert_eq!(reader.seq_names(), Ok(vec!["chr1".to_string(), "chr2".to_string(), "chr3".to_string()]));