Struct rust_htslib::bam::record::Record

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

A BAM record.

Fields

inner: bam1_t

Methods

impl Record

pub fn new() -> Self

Create an empty BAM record.

pub fn from_inner(from: *mut bam1_t) -> Self

pub fn from_sam(header_view: &mut HeaderView, sam: &[u8]) -> Result<Record>

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

pub fn inner(&self) -> &bam1_t

pub fn tid(&self) -> i32

Get target id.

pub fn set_tid(&mut self, tid: i32)

Set target id.

pub fn pos(&self) -> i64

Get position (0-based).

pub fn set_pos(&mut self, pos: i64)

Set position (0-based).

pub fn bin(&self) -> u16

pub fn set_bin(&mut self, bin: u16)

pub fn mapq(&self) -> u8

Get MAPQ.

pub fn set_mapq(&mut self, mapq: u8)

Set MAPQ.

pub fn flags(&self) -> u16

Get raw flags.

pub fn set_flags(&mut self, flags: u16)

Set raw flags.

pub fn unset_flags(&mut self)

Unset all flags.

pub fn mtid(&self) -> i32

Get target id of mate.

pub fn set_mtid(&mut self, mtid: i32)

Set target id of mate.

pub fn mpos(&self) -> i64

Get mate position.

pub fn set_mpos(&mut self, mpos: i64)

Set mate position.

pub fn insert_size(&self) -> i64

Get insert size.

pub fn set_insert_size(&mut self, insert_size: i64)

Set insert size.

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

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

pub fn set_data(&mut self, new_data: &[u8])

Set the variable length data buffer

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

Set variable length data (qname, cigar, seq, qual). The aux data is left unchanged. qual is Phred-scaled quality values, without any offset. NOTE: seq.len() must equal qual.len() or this method will panic. If you don't have quality values use let quals = vec![ 255 as u8; seq.len()]; as a placeholder that will be recognized as missing QVs by samtools.

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

Replace current qname with a new one.

pub fn cigar_len(&self) -> usize

pub fn raw_cigar(&self) -> &[u32]

Get reference to raw cigar string representation (as stored in BAM file). Usually, the method Record::cigar should be used instead.

pub fn cigar(&self) -> CigarStringView

Return unpacked cigar string. This will create a fresh copy the Cigar data.

pub fn cigar_cached(&self) -> Option<&CigarStringView>

pub fn cache_cigar(&mut self)

Decode the cigar string and cache it inside the Record

pub fn seq(&self) -> Seq

Get read sequence. Complexity: O(1).

pub 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).

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

Get auxiliary data (tags).

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

Add auxiliary data.

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

pub fn is_paired(&self) -> bool

pub fn set_paired(&mut self)

pub fn unset_paired(&mut self)

pub fn is_proper_pair(&self) -> bool

pub fn set_proper_pair(&mut self)

pub fn unset_proper_pair(&mut self)

pub fn is_unmapped(&self) -> bool

pub fn set_unmapped(&mut self)

pub fn unset_unmapped(&mut self)

pub fn is_mate_unmapped(&self) -> bool

pub fn set_mate_unmapped(&mut self)

pub fn unset_mate_unmapped(&mut self)

pub fn is_reverse(&self) -> bool

pub fn set_reverse(&mut self)

pub fn unset_reverse(&mut self)

pub fn is_mate_reverse(&self) -> bool

pub fn set_mate_reverse(&mut self)

pub fn unset_mate_reverse(&mut self)

pub fn is_first_in_template(&self) -> bool

pub fn set_first_in_template(&mut self)

pub fn unset_first_in_template(&mut self)

pub fn is_last_in_template(&self) -> bool

pub fn set_last_in_template(&mut self)

pub fn unset_last_in_template(&mut self)

pub fn is_secondary(&self) -> bool

pub fn set_secondary(&mut self)

pub fn unset_secondary(&mut self)

pub fn is_quality_check_failed(&self) -> bool

pub fn set_quality_check_failed(&mut self)

pub fn unset_quality_check_failed(&mut self)

pub fn is_duplicate(&self) -> bool

pub fn set_duplicate(&mut self)

pub fn unset_duplicate(&mut self)

pub fn is_supplementary(&self) -> bool

pub fn set_supplementary(&mut self)

pub fn unset_supplementary(&mut self)

Trait Implementations

impl BamRecordExtensions for Record

fn aligned_blocks(&self) -> Vec<[i64; 2]>

get a list of start and end positions of aligned gapless blocks

fn introns(&self) -> Vec<[i64; 2]>

find intron positions (start, stop)

fn aligned_pairs(&self) -> Vec<[i64; 2]>

a list of aligned read and reference positions

fn aligned_pairs_full(&self) -> Vec<[Option<i64>; 2]>

a list of aligned read and reference positions

fn cigar_stats_nucleotides(&self) -> HashMap<Cigar, i32>

the number of nucleotides covered by each Cigar:: possibility

fn cigar_stats_blocks(&self) -> HashMap<Cigar, i32>

the number of occurances of each each Cigar:: possibility

fn reference_positions(&self) -> Vec<i64>

a Vec of reference positions that this read aligns to

fn reference_positions_full(&self) -> Vec<Option<i64>>

a Vec of reference positions that this read aligns to

fn reference_start(&self) -> i64

left most aligned reference position of the read on the reference genome.

fn reference_end(&self) -> i64

right most aligned reference position of the read on the reference genome.

fn seq_len_from_cigar(&self, include_hard_clip: bool) -> usize

infer the query length from the cigar string, optionally include hard clipped bases

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 Debug for Record

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

Formats the value using the given formatter.

impl Default for Record

fn default() -> Self

Returns the "default value" for a type.

impl Drop for Record

fn drop(&mut self)

Executes the destructor for this type.

impl Eq for Record

impl PartialEq<Record> for Record

fn eq(&self, other: &Record) -> bool

This method tests for self and other values to be equal, and is used by ==.

#[must_use]fn ne(&self, other: &Rhs) -> bool

This method tests for !=.

impl Send for Record

impl SequenceRead for Record

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

fn base(&self, i: usize) -> u8

fn base_qual(&self, i: usize) -> u8

fn len(&self) -> usize

impl Sync for Record