Struct FiberseqData 

pub struct FiberseqData {
    pub record: Record,
    pub annotations: MolecularAnnotations,
    pub ec: f32,
    pub target_name: String,
    pub rg: String,
    pub center_position: Option<CenterPosition>,
}

Fields

record: Record

annotations: MolecularAnnotations

ec: f32

target_name: String

rg: String

center_position: Option<CenterPosition>

Implementations

impl FiberseqData

pub fn new( record: Record, target_name: Option<&String>, filters: &FiberFilters, ) -> Self

pub fn dict_from_head_view(head_view: &HeaderView) -> HashMap<i32, String>

pub fn target_name_from_tid( tid: i32, target_dict: &HashMap<i32, String>, ) -> Option<&String>

pub fn from_records( records: Vec<Record>, head_view: &HeaderView, filters: &FiberFilters, ) -> Vec<Self>

pub fn msp(&self) -> AnnotationTypeView<'_>

View over msp annotations derived from self.annotations.

pub fn nuc(&self) -> AnnotationTypeView<'_>

View over nuc annotations derived from self.annotations.

pub fn m6a(&self) -> AnnotationTypeView<'_>

View over m6a annotations derived from self.annotations.

pub fn cpg(&self) -> AnnotationTypeView<'_>

View over cpg annotations derived from self.annotations.

pub fn fire(&self) -> AnnotationTypeView<'_>

View over fire annotations derived from self.annotations.

pub fn serialize_annotations(&mut self)

Flush self.annotations onto the record’s MA-family aux tags. The single write path for subcommands that edit nuc/msp/fire annotations; call this, then hand the record to the BAM writer.

MM/ML are deliberately left untouched: this is an edit path, not a basemod producer, so the record’s original MM/ML bytes pass through byte-identically. Basemod types (m6a/cpg) are Encoding::MmMl (set when they were read), so write_record excludes them from the MA tag rather than writing basemod calls there too. Producers that synthesize or modify basemods must use ma_io::write_record_with_basemods instead.

pub fn get_qname(&self) -> String

pub fn get_rq(&self) -> Option<f32>

pub fn platform(&self) -> SeqPlatform

Detect the sequencing platform (PacBio vs ONT) for this read from its aux tags, falling back to the read name if those were stripped.

pub fn get_hp(&self) -> String

pub fn write_msp(&self, reference: bool) -> String

pub fn write_nuc(&self, reference: bool) -> String

pub fn write_m6a(&self, reference: bool) -> String

pub fn write_cpg(&self, reference: bool) -> String

pub fn to_bed12( &self, reference: bool, starts: &[Option<i64>], lengths: &[Option<i64>], color: &str, ) -> String

pub fn all_header(simplify: bool, quality: bool) -> String

pub fn write_all(&self, simplify: bool, quality: bool) -> String

Trait Implementations

impl Clone for FiberseqData

fn clone(&self) -> FiberseqData

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for FiberseqData

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

Formats the value using the given formatter.

impl PartialEq for FiberseqData

fn eq(&self, other: &FiberseqData) -> bool

Equality operator ==.

fn ne(&self, other: &Rhs) -> bool

Inequality operator !=.

impl StructuralPartialEq for FiberseqData