Struct varlociraptor::estimation::alignment_properties::AlignmentProperties

pub struct AlignmentProperties { /* fields omitted */ }

Implementations

impl AlignmentProperties

pub fn default(insert_size: Option<InsertSize>) -> Self

Constructs a dummy instance where all bases are feasible.

pub fn update_max_cigar_ops_len(&mut self, record: &Record) -> (bool, bool)

Update maximum observed cigar operation lengths. Return whether any D, I, S, or H operation was found in the cigar string.

pub fn estimate<R: Read>(bam: &mut R) -> Result<Self>

Estimate AlignmentProperties from first 10000 fragments of bam file. Only reads that are mapped, not duplicates and where quality checks passed are taken.

pub fn feasible_bases(&self, read_len: u32, variant: &Variant) -> u32

Number of bases that are feasible for overlapping the variant.

pub fn insert_size(&self) -> &InsertSize

Trait Implementations

impl Clone for AlignmentProperties

fn clone(&self) -> AlignmentProperties

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Copy for AlignmentProperties

impl Debug for AlignmentProperties

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

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for AlignmentProperties

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.

impl Serialize for AlignmentProperties

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

Serialize this value into the given Serde serializer.