Struct IndexedFasta 

pub struct IndexedFasta<S: ReadSeek = BoxedSource> { /* private fields */ }

Random access to an indexed FASTA file.

The source only has to be Read and Seek, so the same code serves a plain file and a BGZF-compressed one — crate::bgzf::BgzfReader seeks in uncompressed coordinates, which is the coordinate system a .fai uses.

Implementations

impl IndexedFasta<BoxedSource>

pub fn open<P: AsRef<Path>>(path: P) -> Result<IndexedFasta>

Open a FASTA file, loading <path>.fai if it exists or building the index in memory if it does not.

Handles plain and BGZF-compressed FASTA. For BGZF it uses <path>.gzi when present and otherwise builds one in memory, which is a header-only scan.

pub fn with_index<P: AsRef<Path>>( path: P, index: FastaIndex, ) -> Result<IndexedFasta>

Open a FASTA file with an index that is already in hand.

impl<S: ReadSeek> IndexedFasta<S>

pub fn from_source(source: S, index: FastaIndex) -> IndexedFasta<S>

Use an arbitrary seekable source, for data that is not in a file.

pub fn index(&self) -> &FastaIndex

The index in use.

pub fn path(&self) -> &Path

The path of the FASTA file.

pub fn fetch(&mut self, name: &str) -> Result<Sequence>

Fetch a whole sequence by name.

pub fn fetch_region( &mut self, name: &str, start: u64, end: u64, ) -> Result<Sequence>

Fetch the half-open, 0-based region start..end.

Note that command line tools such as samtools faidx use 1-based inclusive coordinates: chr1:11-20 is fetch_region("chr1", 10, 20).

pub fn fetch_locus(&mut self, locus: &str) -> Result<Sequence>

Fetch a region given as name, name:start-end or name:start..end using 1-based inclusive coordinates, as command line tools do.

let mut fasta = IndexedFasta::open("ref.fa")?;
let first_ten = fasta.fetch_locus("chr1:1-10")?;
assert_eq!(first_ten.len(), 10);