Struct PafRecord

pub struct PafRecord { /* private fields */ }

Struct representing a PAF record.

Implementations

impl PafRecord

pub fn new( query_name: String, query_len: u32, query_start: u32, query_end: u32, strand: char, target_name: String, target_len: u32, target_start: u32, target_end: u32, residue_matches: u32, alignment_block_len: u32, mapping_quality: u8, optional: HashMap<String, Tag>, ) -> PafRecord

Create a new PAF record.

pub fn query_name(&self) -> &str

Get the query name.

pub fn query_len(&self) -> u32

Get the query length.

pub fn query_start(&self) -> u32

Get the query start position.

pub fn query_end(&self) -> u32

Get the query end position.

pub fn target_name(&self) -> &str

Get the target name.

pub fn target_len(&self) -> u32

Get the target length.

pub fn target_start(&self) -> u32

Get the target start position.

pub fn target_end(&self) -> u32

Get the target end position.

pub fn residue_matches(&self) -> u32

Get the number of residue matches.

pub fn alignment_block_len(&self) -> u32

Get the alignment block length.

pub fn mapping_quality(&self) -> u8

Get the mapping quality.

pub fn strand(&self) -> char

Get the strand.

pub fn optional_fields(&self) -> &HashMap<String, Tag>

Get all the optional fields.

pub fn tp(&self) -> Option<&char>

Get type of aln: P/primary, S/secondary and I,i/inversion.

pub fn cm(&self) -> Option<&i64>

Get number of minimizers on the chain

pub fn s1(&self) -> Option<&i64>

Get chaining score.

pub fn s2(&self) -> Option<&i64>

Get chaining score of the best secondary chain.

pub fn nm(&self) -> Option<&i64>

Get total number of mismatches and gaps in the alignment.

pub fn md(&self) -> Option<&String>

Get the ref sequence in the alignment.

pub fn as_(&self) -> Option<&i64>

Get DP alignment score.

pub fn sa(&self) -> Option<&String>

Get a list of other supplementary alignments.

pub fn ms(&self) -> Option<&i64>

Get DP score of the max scoring segment in the alignment.

pub fn nn(&self) -> Option<&i64>

Get number of ambiguous bases in the alignment.

pub fn ts(&self) -> Option<&char>

Get transcript strand (splice mode only).

pub fn cg(&self) -> Option<&String>

Get CIGAR string (only in PAF).

pub fn cs(&self) -> Option<&String>

Get difference string.

pub fn dv(&self) -> Option<&f64>

Get approximate per-base sequence divergence.

pub fn de(&self) -> Option<&f64>

Get gap-compressed per-base sequence divergence.

pub fn rl(&self) -> Option<&i64>

Get length of query regions harboring repetitive seeds.

Trait Implementations

impl Debug for PafRecord

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

Formats the value using the given formatter.