PileupColumn

Represents a single pileup column

struct PileupColumn (

R

) {

char reference_base();

size_t coverage();

int ref_id();

ulong position();

auto reads_starting_here();

auto base_qualities();

auto read_qualities();

}

Members

Functions

base_qualities auto base_qualities(): Shortcut for map!(read => read.current_base_quality)(reads)
bases auto bases(): Shortcut for map!(read => read.current_base)(reads)
coverage size_t coverage(): Coverage at this position (equals to number of reads)
position ulong position(): Position on the reference
read_qualities auto read_qualities(): Shortcut for map!(read => read.mapping_quality)(reads)
reads auto reads(): Reads overlapping the position, sorted by coordinate
reads_starting_here auto reads_starting_here(): Reads that have leftmost mapped position at this column
ref_id int ref_id(): Returns reference ID (-1 if unmapped)
reference_base char reference_base(): Reference base. 'N' if not available.

Meta

Source

See Implementation

bio bam pileup classes

functions

manifest constants

useMD

structs