Struct faimm::IndexedFasta

pub struct IndexedFasta { /* fields omitted */ }

The IndexFasta can be used to open a fasta file that has a valid .fai index file.

Methods

impl IndexedFasta

pub fn from_file<P: AsRef<Path>>(path: P) -> Result<Self>

Open a fasta file from path P. It is assumed that it has a valid .fai index file. The .fai file is created by appending .fai to the fasta file.

pub fn view(&self, tid: usize, start: usize, stop: usize) -> Result<FastaView>

Use tid, start and end to calculate a slice on the Fasta file. Use this view to iterate over the bases.

Returns FastaView for the provided chromsome, start, end if successful, Error otherwise.

pub fn view_tid(&self, tid: usize) -> Result<FastaView>

Use tid to return a view of an entire chromosome.

Returns FastaView for the provided chromsome indicated by tid if successful, Error otherwise.

pub fn fai(&self) -> &Fai

Return a reference to the Fai that contains information from the fasta index.

Returns a reference to Fai.