Struct rust_htslib::bam::record::Record

pub struct Record {
    pub inner: *mut bam1_t,
    // some fields omitted
}

A BAM record.

Fields

inner: *mut bam1_t

Methods

impl Record

fn new() -> Self

Create an empty BAM record.

fn from_inner(inner: *mut bam1_t) -> Self

fn inner_mut(&mut self) -> &mut bam1_t

fn inner(&self) -> &bam1_t

fn tid(&self) -> i32

Get target id.

fn set_tid(&mut self, tid: i32)

Set target id.

fn pos(&self) -> i32

Get position (0-based).

fn set_pos(&mut self, pos: i32)

Set position (0-based).

fn bin(&self) -> u16

fn set_bin(&mut self, bin: u16)

fn mapq(&self) -> u8

Get MAPQ.

fn set_mapq(&mut self, mapq: u8)

Set MAPQ.

fn flags(&self) -> u16

Get raw flags.

fn set_flags(&mut self, flags: u16)

Set raw flags.

fn unset_flags(&mut self)

Unset all flags.

fn mtid(&self) -> i32

Get target id of mate.

fn set_mtid(&mut self, mtid: i32)

Set target id of mate.

fn mpos(&self) -> i32

Get mate position.

fn set_mpos(&mut self, mpos: i32)

Set mate position.

fn insert_size(&self) -> i32

Get insert size.

fn set_insert_size(&mut self, insert_size: i32)

Set insert size.

fn qname(&self) -> &[u8]

Get qname (read name). Complexity: O(1).

fn set(&mut self, qname: &[u8], cigar: &CigarString, seq: &[u8], qual: &[u8])

Set variable length data (qname, cigar, seq, qual). Note: Pre-existing aux data will be invalidated if called on an existing record. For this reason, never call push_aux() before set().

fn set_qname(&mut self, new_qname: &[u8])

Replace current qname with a new one. Unlike set(), this preserves all the variable length data including the aux.

fn cigar(&self) -> CigarStringView

Get cigar string. Complexity: O(k) with k being the length of the cigar string.

fn seq(&self) -> Seq

Get read sequence. Complexity: O(1).

fn qual(&self) -> &[u8]

Get base qualities (PHRED-scaled probability that base is wrong). This does not entail any offsets, hence the qualities can be used directly without e.g. subtracting 33. Complexity: O(1).

fn aux(&self, tag: &[u8]) -> Option<Aux>

Get auxiliary data (tags).

fn push_aux(&mut self, tag: &[u8], value: &Aux)

Add auxiliary data. push_aux() should never be called before set().

fn remove_aux(&self, tag: &[u8]) -> bool

fn is_paired(&self) -> bool

fn set_paired(&mut self)

fn is_proper_pair(&self) -> bool

fn set_proper_pair(&mut self)

fn is_unmapped(&self) -> bool

fn set_unmapped(&mut self)

fn is_mate_unmapped(&self) -> bool

fn set_mate_unmapped(&mut self)

fn is_reverse(&self) -> bool

fn set_reverse(&mut self)

fn is_mate_reverse(&self) -> bool

fn set_mate_reverse(&mut self)

fn is_first_in_template(&self) -> bool

fn set_first_in_template(&mut self)

fn is_last_in_template(&self) -> bool

fn set_last_in_template(&mut self)

fn is_secondary(&self) -> bool

fn set_secondary(&mut self)

fn is_quality_check_failed(&self) -> bool

fn set_quality_check_failed(&mut self)

fn is_duplicate(&self) -> bool

fn set_duplicate(&mut self)

fn is_supplementary(&self) -> bool

fn set_supplementary(&mut self)

Trait Implementations

impl Send for Record

impl Sync for Record

impl Clone for Record

fn clone(&self) -> Self

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Drop for Record

fn drop(&mut self)

Executes the destructor for this type.