Struct faimm::Fai

pub struct Fai { /* fields omitted */ }

The object that stores the parsed fasta index file. You can use it to map chromosome names to indexes and lookup offsets for chr-start:end coordinates

Methods

impl Fai

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

Open a fasta index file from path P.

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

Calculate the slice coordinates (byte offsets). tid is the index of the chromosome (lookup with Fai::tid if necessary. start, end: zero based coordinates of the requested range.

Returns an tuple (start, end) if successful. io::Error otherwise.

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

Calculate the slice coordinates (byte offsets). tid is the index of the chromosome (lookup with Fai::tid if necessary.

Returns an tuple (start, end) if successful. io::Error otherwise.

pub fn tid(&self, name: &str) -> Option<usize>

Return the index of the chromosome by name in the fasta index.

Returns the position of chr name if succesful, None otherwise.

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

Return the index of a chromosome in the fasta index.

Returns the size in bases as usize.

pub fn name(&self, tid: usize) -> Result<&String>

Return the name of the chromomsome at index tid

pub fn names(&self) -> Vec<&str>

Return the names of the chromosomes from the fasta index in the same order as in the .fai. You can use Fai::tid to map it back to an index.

Returns a Vec<&str> with the chromosome names.

Trait Implementations

impl Debug for Fai

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

Formats the value using the given formatter.

impl Clone for Fai

fn clone(&self) -> Fai

Returns a copy of the value.

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

Performs copy-assignment from source.