Struct FastaDir

pub struct FastaDir { /* private fields */ }

This class provides a simple key-value interface to a directory of compressed FASTA files.

Sequences are stored in dated FASTA files. Dating the files enables compact storage with multiple releases (using hard links) and efficient incremental updtes and transfers (e.g., via rsync). The FASTA files are compressed with block gzip, enabling fast random access to arbitrary regions of even large (chromosome-sized) sequences.

When the key is a hash based on sequence (e.g., SHA512), the combination provides a convenient non-redundant storage of sequences with fast access to sequences and sequence slices, compact storage and easy replication.

Implementations

impl FastaDir

pub fn new<P>(root_dir: P) -> Result<Self, Error>

where P: AsRef<Path>,

Initialize new FastaDir, will open connection to the database.

pub fn schema_version(&self) -> u32

Schema version as read from the database.

pub fn fetch_seqinfo(&self, seq_id: &str) -> Result<SeqInfoRecord, Error>

Load SeqInfoRecord from database.

pub fn fetch_sequence(&self, seq_id: &str) -> Result<String, Error>

Load complete sequence from FASTA directory.

pub fn fetch_sequence_part( &self, seq_id: &str, begin: Option<usize>, end: Option<usize>, ) -> Result<String, Error>

Load sequence fragment from FASTA directory.

Trait Implementations

impl Debug for FastaDir

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

Formats the value using the given formatter.