Struct QueryHeader 

pub struct QueryHeader {
    pub source: Option<String>,
    pub contigs: Vec<Contig>,
    pub naming_convention: NamingConvention,
    pub md5_set: HashSet<String>,
    pub name_length_set: HashSet<(String, u64)>,
    pub alias_length_set: HashSet<(String, u64)>,
    pub signature: Option<String>,
}

A query header extracted from a BAM/SAM/CRAM file

Fields

source: Option<String>

Source file path (if known)

contigs: Vec<Contig>

All contigs from @SQ lines

naming_convention: NamingConvention

Detected naming convention

md5_set: HashSet<String>

Set of MD5s present in header

name_length_set: HashSet<(String, u64)>

Set of (exact_name, length) pairs for matching

alias_length_set: HashSet<(String, u64)>

Set of (alias, length) pairs for alias-based matching

signature: Option<String>

Signature for exact matching

Implementations

impl QueryHeader

pub fn new(contigs: Vec<Contig>) -> Self

pub fn with_source(self, source: impl Into<String>) -> Self

pub fn rebuild_indexes(&mut self)

pub fn has_md5s(&self) -> bool

Check if header has MD5 information

pub fn md5_coverage(&self) -> f64

Fraction of contigs with MD5 checksums

Trait Implementations

impl Clone for QueryHeader

fn clone(&self) -> QueryHeader

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for QueryHeader

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for QueryHeader

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Serialize for QueryHeader

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.