Struct bam::header::Header [−][src]
pub struct Header { /* fields omitted */ }
BAM/SAM Header.
You can modify it by pushing new lines using push_entry, push_comment and push_line.
You cannot remove lines, but you can create a new header and push there only a subset of lines.
Implementations
impl Header
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pub fn new() -> Header
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Creates an empty header.
pub fn lines(&self) -> Iter<'_, HeaderLine>
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Iterator over lines.
pub fn push_entry(&mut self, entry: HeaderEntry) -> Result<(), String>
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Pushes a new header entry.
Returns an error if the same reference appears twice or @SQ line has an incorrect format.
pub fn push_comment(&mut self, comment: String)
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Pushes a new comment.
pub fn push_line(&mut self, line: &str) -> Result<()>
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Pushes a lines to the header.
pub fn write_text<W: Write>(&self, writer: &mut W) -> Result<()>
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Write header in SAM format.
pub fn write_bam<W: Write>(&self, writer: &mut W) -> Result<()>
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Writes header in an uncompressed BAM format.
pub fn from_bam<R: Read>(stream: &mut R) -> Result<Self>
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Parse uncompressed BAM header, starting with magic b"BAM\1"
.
pub fn n_references(&self) -> usize
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Returns the number of reference sequences in the BAM file.
pub fn reference_name(&self, ref_id: u32) -> Option<&str>
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Returns the name of the reference with ref_id
(0-based).
Returns None if there is no such reference
pub fn reference_len(&self, ref_id: u32) -> Option<u32>
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Returns the length of the reference with ref_id
(0-based).
Returns None if there is no such reference
pub fn reference_id(&self, ref_name: &str) -> Option<u32>
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Returns reference id from its name, if possible.
pub fn reference_names(&self) -> &[String]
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Returns reference names.
pub fn reference_lengths(&self) -> &[u32]
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Returns reference names.
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Header
impl Send for Header
impl Sync for Header
impl Unpin for Header
impl UnwindSafe for Header
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> ToOwned for T where
T: Clone,
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T: Clone,
type Owned = T
The resulting type after obtaining ownership.
pub fn to_owned(&self) -> T
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pub fn clone_into(&self, target: &mut T)
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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>,