Struct GenomeIO

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pub struct GenomeIO<R> { /* private fields */ }

Expand description

FASTA/FASTQ parser

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impl<R: Read> GenomeIO<R>

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pub fn new(reader: R) -> Self

Create a new genome reader

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pub fn read_contig(&mut self) -> Result<Option<(String, Contig)>>

Read next contig without conversion (preserves ASCII)

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pub fn read_contig_converted(&mut self) -> Result<Option<(String, Contig)>>

Read next contig with nucleotide conversion (ASCII -> numeric)

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pub fn read_contig_with_sample( &mut self, ) -> Result<Option<(String, String, String, Contig)>>

Read next contig with parsed sample/contig names (for multi-sample FASTAs) Returns: (full_header, sample_name, contig_name, sequence)

Parses headers in format: >sample#haplotype#chromosome Example: >S288C#1#chrI -> sample=“S288C#1”, contig=“chrI”

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pub fn read_contig_raw(&mut self) -> Result<Option<(String, Contig)>>

Read next contig preserving raw format (including newlines)

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impl GenomeIO<Box<dyn Read>>

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pub fn open<P: AsRef<Path>>(path: P) -> Result<Self>

Open a FASTA file for reading (supports .gz files)

Auto Trait Implementations§

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impl<R> UnwindSafe for GenomeIO<R>
where R: UnwindSafe,

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impl<T> Any for T
where T: 'static + ?Sized,

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impl<T> Borrow<T> for T
where T: ?Sized,

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impl<T> BorrowMut<T> for T
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fn borrow_mut(&mut self) -> &mut T

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impl<T> From<T> for T

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fn from(t: T) -> T

Returns the argument unchanged.

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where U: From<T>,

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Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

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impl<T> IntoEither for T

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fn into_either(self, into_left: bool) -> Either<Self, Self>

Converts self into a Left variant of Either<Self, Self> if into_left is true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more

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fn into_either_with<F>(self, into_left: F) -> Either<Self, Self>
where F: FnOnce(&Self) -> bool,

Converts self into a Left variant of Either<Self, Self> if into_left(&self) returns true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more

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