Struct Record

pub struct Record {
    pub inner: bam1_t,
    /* private fields */
}

A BAM record.

Fields

inner: bam1_t

Implementations

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: &HeaderView, sam: &[u8]) -> Result<Record>

pub fn set_header(&mut self, header: Rc<HeaderView>)

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 strand(&self) -> ReqStrand

Get strand information from record flags.

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_len(&self) -> usize

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]) -> Result<Aux<'_>>

Look up an auxiliary field by its tag.

Only the first two bytes of a given tag are used for the look-up of a field. See Aux for more details.

pub fn aux_iter(&self) -> AuxIter<'_>

Returns an iterator over the auxiliary fields of the record.

When an error occurs, the Err variant will be returned and the iterator will not be able to advance anymore.

pub fn push_aux(&mut self, tag: &[u8], value: Aux<'_>) -> Result<()>

Add auxiliary data.

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

pub fn basemods_iter(&self) -> Result<BaseModificationsIter<'_>>

Access the base modifications associated with this Record through the MM tag. Example:

   use rust_htslib::bam::{Read, Reader, Record};
   let mut bam = Reader::from_path(&"test/base_mods/MM-orient.sam").unwrap();
   let mut mod_count = 0;
   for r in bam.records() {
       let record = r.unwrap();
       if let Ok(mods) = record.basemods_iter() {
           // print metadata for the modifications present in this record
           for mod_code in mods.recorded() {
               if let Ok(mod_metadata) = mods.query_type(*mod_code) {
                   println!("mod found with code {}/{} flags: [{} {} {}]",
                             mod_code, *mod_code as u8 as char,
                             mod_metadata.strand, mod_metadata.implicit, mod_metadata.canonical as u8 as char);
               }
           }

           // iterate over the modifications in this record
           // the modifications are returned as a tuple with the
           // position within SEQ and an hts_base_mod struct
           for res in mods {
               if let Ok( (position, m) ) = res {
                   println!("{} {},{}", position, m.modified_base as u8 as char, m.qual);
                   mod_count += 1;
               }
           }
       };
   }
   assert_eq!(mod_count, 14);

pub fn basemods_position_iter( &self, ) -> Result<BaseModificationsPositionIter<'_>>

An iterator that returns all of the modifications for each position as a vector. This is useful for the case where multiple possible modifications can be annotated at a single position (for example a C could be 5-mC or 5-hmC)

pub fn read_pair_orientation(&self) -> SequenceReadPairOrientation

Infer read pair orientation from record. Returns SequenceReadPairOrientation::None if record is not paired, mates are not mapping to the same contig, or mates start at the same position.

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 AbstractInterval for Record

fn contig(&self) -> &str

Return contig name. Panics if record does not know its header (which happens if it has not been read from a file).

fn range(&self) -> Range<Position>

Return genomic range covered by alignment. Panics if Record::cache_cigar() has not been called first or Record::pos() is less than zero.

fn contains<L>(&self, locus: L) -> bool

where L: AbstractLocus,

Return true if interval contains given locus.

impl BamRecordExtensions for Record

fn reference_end(&self) -> i64

Calculate the rightmost base position of an alignment on the reference genome. Returns the coordinate of the first base after the alignment (0-based).

fn aligned_blocks(&self) -> IterAlignedBlocks

iterator over start and end positions of aligned gapless blocks

fn introns(&self) -> IterIntrons

This scans the CIGAR for reference skips and reports their positions. It does not inspect the reported regions for actual splice sites. pysam: get_introns

fn aligned_block_pairs(&self) -> IterAlignedBlockPairs

Iter over <([read_start, read_stop], [genome_start, genome_stop]) blocks of continously aligned reads.

fn aligned_pairs(&self) -> IterAlignedPairs

iter aligned read and reference positions on a basepair level

fn aligned_pairs_full(&self) -> IterAlignedPairsFull

iter list of read and reference positions on a basepair level.

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

the number of nucleotides covered by each Cigar::* variant.

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

the number of occurrences of each each Cigar::* variant

fn reference_positions(&self) -> Box<dyn Iterator<Item = i64>>

iter over reference positions that this read aligns to

fn reference_positions_full(&self) -> Box<dyn Iterator<Item = Option<i64>>>

iter over 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 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 PartialEq for Record

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

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl SequenceRead for Record

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

Read name.

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

Base at position i in the read.

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

Base quality at position i in the read.

fn len(&self) -> usize

Read length.

fn is_empty(&self) -> bool

Return true if read is empty.

impl Eq for Record

impl Send for Record

impl Sync for Record