Struct Flags 

pub struct Flags { /* private fields */ }

An ad hoc bitvector for flags in AlignmentBlock.

Implementations

impl Flags

pub const NUM_FLAGS: usize = 6

Number of flags per alignment.

pub const FLAG_PAIR_IS_NEXT: usize = 0

Flag: Pair is the next fragment in the read pair.

pub const FLAG_PAIR_IS_PROPER: usize = 1

Flag: The the alignment is properly paired.

pub const FLAG_HAS_MAPQ: usize = 2

Flag: A mapping quality score is present.

pub const FLAG_HAS_SCORE: usize = 3

Flag: An alignment score is present.

pub const FLAG_FULL_ALIGNMENT: usize = 4

Flag: This is an alignment of the entire query sequence.

We do not encode the lengths of the unaligned flanks.

pub const FLAG_EXACT_ALIGNMENT: usize = 5

Flag: This is an exact alignment.

We do not encode the difference string, matches, or edits.

pub fn new(num_alignments: usize) -> Self

Creates a new flags object with the given number of alignments. The flags are initialized to zero (false).

pub fn set(&mut self, index: usize, flag: usize, value: bool)

Sets the given flag.

Arguments

• index: The index of the alignment.
• flag: The flag to set.
• value: The value to set the flag to.

pub fn get(&self, index: usize, flag: usize) -> bool

Gets the value of the given flag.

Arguments

• index: The index of the alignment.
• flag: The flag to get.

pub fn bytes(&self) -> usize

Returns the number of bytes used to store the flags.

Trait Implementations

impl AsRef<[u8]> for Flags

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

Converts this type into a shared reference of the (usually inferred) input type.

impl Clone for Flags

fn clone(&self) -> Flags

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Flags

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

Formats the value using the given formatter.

impl From<Vec<u8>> for Flags

fn from(bits: Vec<u8>) -> Self

Converts to this type from the input type.