Struct SamRecord 

pub struct SamRecord {
    pub qname: String,
    pub flag: u16,
    pub rname: String,
    pub pos: i32,
    pub mapq: u8,
    pub cigar: Vec<CigarOp>,
    pub rnext: String,
    pub pnext: i32,
    pub tlen: i32,
    pub seq: Vec<u8>,
    pub qual: Vec<u8>,
    pub tags: HashMap<String, TagValue>,
}

SAM alignment record

This struct is identical to BAM’s BamRecord but parsed from text instead of binary.

Fields

qname: String

Query template name

flag: u16

Bitwise FLAG

rname: String

Reference sequence name

pos: i32

1-based leftmost mapping position (0 for unmapped)

mapq: u8

Mapping quality (255 if unavailable)

cigar: Vec<CigarOp>

CIGAR string

rnext: String

Reference name of mate/next read

pnext: i32

Position of mate/next read (0 if unavailable)

tlen: i32

Template length

seq: Vec<u8>

Segment sequence (empty if unavailable)

qual: Vec<u8>

Phred-scaled base qualities (empty if unavailable)

tags: HashMap<String, TagValue>

Optional tags

Implementations

impl SamRecord

pub fn is_paired(&self) -> bool

Check if read is paired

pub fn is_proper_pair(&self) -> bool

Check if read is mapped in proper pair

pub fn is_unmapped(&self) -> bool

Check if read is unmapped

pub fn is_mate_unmapped(&self) -> bool

Check if mate is unmapped

pub fn is_reverse(&self) -> bool

Check if read is reverse strand

pub fn is_mate_reverse(&self) -> bool

Check if mate is reverse strand

pub fn is_first_in_pair(&self) -> bool

Check if read is first in pair

pub fn is_second_in_pair(&self) -> bool

Check if read is second in pair

pub fn is_secondary(&self) -> bool

Check if alignment is secondary

pub fn is_qc_fail(&self) -> bool

Check if read fails quality checks

pub fn is_duplicate(&self) -> bool

Check if read is a PCR or optical duplicate

pub fn is_supplementary(&self) -> bool

Check if alignment is supplementary

pub fn cigar_string(&self) -> String

Get CIGAR string representation

pub fn seq_string(&self) -> String

Get sequence as string

Trait Implementations

impl Clone for SamRecord

fn clone(&self) -> SamRecord

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for SamRecord

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl From<&SamRecord> for GenomicInterval

fn from(record: &SamRecord) -> Self

Converts to this type from the input type.

impl From<SamRecord> for GenomicInterval

fn from(record: SamRecord) -> Self

Converts to this type from the input type.