Struct seq_io::fastq::Reader
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pub struct Reader<R: Read, S = DoubleUntil8M> { /* fields omitted */ }
FASTQ parser.
Methods
impl<R> Reader<R, DoubleUntil8M> where
R: Read,
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R: Read,
fn new(reader: R) -> Reader<R, DoubleUntil8M>
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Creates a new reader with the default buffer size of 68 KB
Example:
use seq_io::fastq::{Reader,Record}; let fastq = b"@id\nACGT\n+\nIIII"; let mut reader = Reader::new(&fastq[..]); let record = reader.next().unwrap().unwrap(); assert_eq!(record.id(), Ok("id"))
fn with_capacity(reader: R, capacity: usize) -> Reader<R, DoubleUntil8M>
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Creates a reader with the given buffer size
impl Reader<File, DoubleUntil8M>
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fn from_path<P: AsRef<Path>>(path: P) -> Result<Reader<File>>
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Creates a reader from a file path.
Example:
use seq_io::fastq::Reader; let mut reader = Reader::from_path("seqs.fastq").unwrap(); // (... do something with the reader)
impl<R, S> Reader<R, S> where
R: Read,
S: BufStrategy,
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R: Read,
S: BufStrategy,
fn with_cap_and_strategy(reader: R, cap: usize, buf_strategy: S) -> Reader<R, S>
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Creates a new reader with a given buffer capacity and growth strategy. See here for an example using the FASTA reader, but otherwise equivalent.
fn next<'a>(&'a mut self) -> Option<Result<RefRecord<'a>, Error>>
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Searches the next FASTQ record and returns a RefRecord that borrows its data from the underlying buffer of this reader.
Example:
use seq_io::fastq::{Reader,Record}; let mut reader = Reader::from_path("seqs.fastq").unwrap(); while let Some(record) = reader.next() { let record = record.unwrap(); println!("{}", record.id().unwrap()); }
fn read_record_set(&mut self, rset: &mut RecordSet) -> Option<Result<(), Error>>
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Updates a RecordSet with new data. The contents of the internal
buffer are just copied over to the record set and the positions of all records are found.
Old data will be erased. Returns None
if the input reached its end.
fn position(&self) -> &Position
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Returns the current position (useful with seek()
)
Example
use seq_io::fastq::{Reader,Position}; let fastq = b"@id1 ACGT + IIII @id2 TGCA + IIII"; let mut reader = Reader::new(&fastq[..]); // skip one record reader.next().unwrap(); // second position reader.next().unwrap(); assert_eq!(reader.position(), &Position::new(5, 17));
fn records(&mut self) -> RecordsIter<R, S>
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Returns a borrowed iterator over all FASTQ records. The records
are owned (OwnedRecord
), this is therefore slower than using
Reader::next()
.
Example
use seq_io::fastq::{Reader,OwnedRecord}; let fastq = b"@id1 ACGT + IIII @id2 TGCA + IIII"; let mut reader = Reader::new(&fastq[..]); let records: Result<Vec<_>, _> = reader .records() .collect(); assert_eq!(records.unwrap(), vec![ OwnedRecord {head: b"id1".to_vec(), seq: b"ACGT".to_vec(), qual: b"IIII".to_vec()}, OwnedRecord {head: b"id2".to_vec(), seq: b"TGCA".to_vec(), qual: b"IIII".to_vec()} ] );
fn into_records(self) -> RecordsIntoIter<R, S>
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Returns an iterator over all FASTQ records like Reader::records()
,
but with the difference that it owns the underlying reader.
impl<R, S> Reader<R, S> where
R: Read + Seek,
S: BufStrategy,
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R: Read + Seek,
S: BufStrategy,
fn seek(&mut self, pos: &Position) -> Result<(), Error>
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Seeks to a specified position.
Keep the underyling buffer if the seek position is found within it, otherwise it has to be
discarded.
If an error was returned before, seeking to that position will return the same error.
The same is not always true with None
. If there is no newline character at the end of the
file, the last record will be returned instead of None
.
Example
use seq_io::fastq::{Reader,Position,OwnedRecord}; use std::io::Cursor; let fastq = b"@id1 ACGT + IIII @id2 TGCA + IIII"; let mut cursor = Cursor::new(&fastq[..]); let mut reader = Reader::new(cursor); // read the first record and get its position let record1 = reader.next().unwrap().unwrap().to_owned_record(); let pos1 = reader.position().to_owned(); // read the second record reader.next().unwrap().unwrap(); // now seek to position of first record reader.seek(&pos1); assert_eq!(reader.next().unwrap().unwrap().to_owned_record(), record1);
Trait Implementations
impl<R, S> Reader for Reader<R, S> where
R: Read,
S: BufStrategy + Send,
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R: Read,
S: BufStrategy + Send,