Struct twobit::convert::fasta::FastaReader

pub struct FastaReader { /* private fields */ }

Read a Fasta file and make the extracted information available

Implementations

impl FastaReader

pub fn mem_open(data: Vec<u8>) -> Result<Self, Error>

Read data from a Fasta file that is stored in a Vec<u8>.

pub fn open<P: AsRef<Path>>(file_path: P) -> Result<Self, Error>

Open a Fasta file on disk

Trait Implementations

impl<'a> SequenceRead<'a> for FastaReader

fn sequence_lengths(&'a self) -> Result<&'a [SequenceLength], Box<dyn Error>>

Return the names and lengths of the sequences (ideally in a stable order for reproducibility)

fn nucleotides(&self, chr: &str) -> Result<Box<dyn Nucleotides>, Box<dyn Error>>

Return pieces of the actual nucleotide sequence

fn soft_masked_blocks(
    &'a self,
    chr: &str
) -> Result<&'a [Range<usize>], Box<dyn Error>>

Return the soft masked blocks for a sequence

fn hard_masked_blocks(
    &'a self,
    chr: &str
) -> Result<&'a [Range<usize>], Box<dyn Error>>

Return the hard masked blocks for a sequence