Struct PafRecord 

pub struct PafRecord {
    pub query_name: String,
    pub query_len: usize,
    pub query_start: usize,
    pub query_end: usize,
    pub strand: char,
    pub target_name: String,
    pub target_len: usize,
    pub target_start: usize,
    pub target_end: usize,
    pub matches: usize,
    pub block_len: usize,
}

A single PAF alignment record.

Contains the 12 mandatory PAF columns parsed from a single line. Optional tags (columns 13+) are not currently parsed.

Fields

query_name: String

Query sequence name (column 1).

query_len: usize

Query sequence length (column 2).

query_start: usize

Query start position, 0-based (column 3).

query_end: usize

Query end position (column 4).

strand: char

Relative strand: ‘+’ or ‘-’ (column 5).

target_name: String

Target sequence name (column 6).

target_len: usize

Target sequence length (column 7).

target_start: usize

Target start position (column 8).

target_end: usize

Target end position (column 9).

matches: usize

Number of matching bases (column 10).

block_len: usize

Alignment block length (column 11).

Implementations

impl PafRecord

pub fn parse_line(line: &str) -> Result<Self>

Parses a PAF record from a tab-separated line.

Arguments

• line - A single line from a PAF file

Returns

A parsed PafRecord, or an error if the line is malformed.

Errors

Returns an error if:

• The line has fewer than 12 fields
• Any numeric field cannot be parsed

pub fn calculate_identity(&self) -> f64

Calculates alignment identity percentage.

Identity = (matching bases / alignment block length) × 100

Returns

Identity percentage (0-100), or 0 if block_len is 0.

pub fn calculate_coverage(&self) -> f64

Calculates target coverage percentage.

Coverage = (aligned target length / total target length) × 100

Returns

Coverage percentage (0-100), or 0 if target_len is 0.

Trait Implementations

impl Clone for PafRecord

fn clone(&self) -> PafRecord

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for PafRecord

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

Formats the value using the given formatter.