Struct needletail::formats::FastqRecord

pub struct FastqRecord<'a> {
    pub id: &'a [u8],
    pub seq: &'a [u8],
    pub id2: &'a [u8],
    pub qual: &'a [u8],
}

A zero-copy reference to a FASTQ record in a buffer.

Fields

id: &'a [u8]

seq: &'a [u8]

id2: &'a [u8]

qual: &'a [u8]

Trait Implementations

impl<'a> Sequence<'a> for FastqRecord<'a>

fn sequence(&self) -> &'a [u8]

fn strip_returns(&'a self) -> Cow<'a, [u8]>

Remove newlines from the sequence; this handles \r, \n, and \r\n and removes internal newlines in addition to ones at the end. Primarily used for FASTA multiline records, but can also help process (the much rarer) multiline FASTQs. Always use before iteration methods below to ensure no newlines are being returned with e.g. .kmers.

fn reverse_complement(&'a self) -> Vec<u8>

Returns the reverse complement of a sequence. Biologically this is equivalent to the sequence of the strand opposite the one you pass in.

fn normalize(&'a self, iupac: bool) -> Cow<'a, [u8]>

[Nucleic Acids] Normalizes the sequence. See documentation for needletail::sequence::normalize. Do not use on amino acid sequences. Note that this returns a Cow so you may have to coerce to a Vec or &u8 as necessary.

Important traits for CanonicalKmers<'a>

impl<'a> Iterator for CanonicalKmers<'a> type Item = (usize, &'a [u8], bool);

fn canonical_kmers(
    &'a self,
    k: u8,
    reverse_complement: &'a [u8]
) -> CanonicalKmers<'a>

[Nucleic Acids] Returns an iterator over the sequence that skips non-ACGT bases and returns a tuple containing (position, the canonicalized kmer, if the sequence is the complement of the original).

Important traits for Kmers<'a>

impl<'a> Iterator for Kmers<'a> type Item = &'a [u8];

fn kmers(&'a self, k: u8) -> Kmers<'a>

Returns an iterator that returns a sliding window of k-sized sequences (k-mers). Does not skip whitespace or correct bases in the original sequence so .normalize or .strip_returns may be appropriate to use first.

Important traits for BitNuclKmer<'a>

impl<'a> Iterator for BitNuclKmer<'a> type Item = (usize, BitKmer, bool);

fn bit_kmers(&'a self, k: u8, canonical: bool) -> BitNuclKmer<'a>

Return an iterator that returns valid kmers in 4-bit form

impl<'a> From<FastqRecord<'a>> for SequenceRecord<'a>

fn from(fastq: FastqRecord<'a>) -> SequenceRecord<'a>

Performs the conversion.

impl<'a> Debug for FastqRecord<'a>

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

Formats the value using the given formatter.