Struct FastaIndex 

pub struct FastaIndex { /* private fields */ }

A parsed or freshly built FASTA index.

Implementations

impl FastaIndex

pub fn build<R: Read>(reader: R) -> Result<FastaIndex>

Build an index by scanning an uncompressed FASTA stream.

Fails with Error::Index when a record has ragged line lengths, since such a file cannot be indexed by arithmetic — exactly as samtools faidx reports it.

pub fn build_from_path<P: AsRef<Path>>(path: P) -> Result<FastaIndex>

Build an index for a FASTA file on disk.

The offsets are always positions in the uncompressed data, so the same .fai describes a file whether or not it is BGZF-compressed — which is exactly how samtools faidx behaves. A BGZF file additionally needs a .gzi to be seekable; IndexedFasta::open takes care of that.

Plain gzip (a single deflate stream, as gzip produces) cannot be randomly accessed at all, and is rejected.

pub fn parse<R: Read>(reader: R) -> Result<FastaIndex>

Parse an existing .fai file.

pub fn from_path<P: AsRef<Path>>(path: P) -> Result<FastaIndex>

Parse a .fai file from disk.

pub fn write<W: Write>(&self, out: &mut W) -> Result<()>

Serialise the index in .fai format.

pub fn write_to_path<P: AsRef<Path>>(&self, fasta_path: P) -> Result<PathBuf>

Write the index next to the FASTA file as <path>.fai.

pub fn get(&self, name: &str) -> Option<&FaiRecord>

Look up a sequence by name.

pub fn records(&self) -> &[FaiRecord]

All records, in file order.

pub fn len(&self) -> usize

Number of indexed sequences.

pub fn is_empty(&self) -> bool

True when the index holds no sequences.

pub fn total_length(&self) -> u64

Sum of all sequence lengths.

Trait Implementations

impl Clone for FastaIndex

fn clone(&self) -> FastaIndex

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for FastaIndex

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

Formats the value using the given formatter.

impl Default for FastaIndex

fn default() -> FastaIndex

Returns the “default value” for a type.