Struct faimm::IndexedFasta [−][src]
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
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impl IndexedFasta
pub fn from_file<P: AsRef<Path>>(path: P) -> Result<Self>
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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>
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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>
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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
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pub fn fai(&self) -> &Fai
Return a reference to the Fai
that contains information from the fasta index.
Returns a reference to Fai
.
Auto Trait Implementations
impl Send for IndexedFasta
impl Send for IndexedFasta
impl Sync for IndexedFasta
impl Sync for IndexedFasta