[−][src]Struct d4_hts::alignment::BamFile
A BAM/CRAM/SAM File
Implementations
impl BamFile
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pub fn set_required_fields(&mut self, flag: u32)
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pub fn reference_path<P: AsRef<Path>>(&self, path: P)
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Set the path to the reference FAI file. Only used for CRAM
pub fn open<P: AsRef<Path>>(path: P) -> Result<Self, AlignmentError>
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Open a BAM/CRAM/SAM file on the disk
pub fn chroms(&self) -> &[(String, usize)]
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pub fn range(
&mut self,
chrom: &str,
from: usize,
to: usize
) -> Result<Ranged<'_>, AlignmentError>
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&mut self,
chrom: &str,
from: usize,
to: usize
) -> Result<Ranged<'_>, AlignmentError>
Trait Implementations
impl<'a> AlignmentReader<'a> for &'a BamFile
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fn start(&self) -> (u32, u32)
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fn get_file(&self) -> &'a BamFile
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fn next(
&self,
buf: *mut bam1_t
) -> Result<Option<Alignment<'a>>, AlignmentError>
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&self,
buf: *mut bam1_t
) -> Result<Option<Alignment<'a>>, AlignmentError>
fn to_alignment_iter(self) -> AlignmentIter<'a, Self>ⓘNotable traits for AlignmentIter<'a, R>
impl<'a, R: AlignmentReader<'a>> Iterator for AlignmentIter<'a, R> type Item = Result<Alignment<'a>, AlignmentError>;
where
Self: Sized,
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Notable traits for AlignmentIter<'a, R>
impl<'a, R: AlignmentReader<'a>> Iterator for AlignmentIter<'a, R> type Item = Result<Alignment<'a>, AlignmentError>;
Self: Sized,
impl Drop for BamFile
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Auto Trait Implementations
impl !RefUnwindSafe for BamFile
impl !Send for BamFile
impl !Sync for BamFile
impl Unpin for BamFile
impl UnwindSafe for BamFile
Blanket Implementations
impl<T> Any for T where
T: 'static + ?Sized,
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T: 'static + ?Sized,
impl<T> Borrow<T> for T where
T: ?Sized,
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T: ?Sized,
impl<T> BorrowMut<T> for T where
T: ?Sized,
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T: ?Sized,
pub fn borrow_mut(&mut self) -> &mut T
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impl<T> From<T> for T
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impl<T, U> Into<U> for T where
U: From<T>,
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U: From<T>,
impl<T, U> TryFrom<U> for T where
U: Into<T>,
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U: Into<T>,
type Error = Infallible
The type returned in the event of a conversion error.
pub fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>
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impl<T, U> TryInto<U> for T where
U: TryFrom<T>,
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U: TryFrom<T>,