PileupRead

Represents a read aligned to a column

struct PileupRead (

Read = bio.std.hts.bam.read.EagerBamRead

) {

bio.std.hts.bam.read.CigarOperation cigar_operation();

uint cigar_operation_offset();

const(bio.std.hts.bam.read.CigarOperation)[] cigar_after();

const(bio.std.hts.bam.read.CigarOperation)[] cigar_before();

char current_base();

ubyte current_base_quality();

int query_offset();

PileupRead dup();

}

Alias This

Members

Functions

cigar_after const(bio.std.hts.bam.read.CigarOperation)[] cigar_after()

CIGAR operations after the current operation

cigar_before const(bio.std.hts.bam.read.CigarOperation)[] cigar_before()

CIGAR operations before the current operation

cigar_operation bio.std.hts.bam.read.CigarOperation cigar_operation()

Current CIGAR operation. One of 'M', '=', 'X', 'D', 'N. Use cigar_after/cigar_before to determine insertions.

cigar_operation_offset uint cigar_operation_offset()

Number of bases consumed from the current CIGAR operation.

current_base char current_base()

If current CIGAR operation is one of 'M', '=', or 'X', returns read base at the current column. Otherwise, returns '-'.

current_base_quality ubyte current_base_quality()

If current CIGAR operation is one of 'M', '=', or 'X', returns Phred-scaled read base quality at the current column. Otherwise, returns 255.

dup PileupRead dup()

Returns duplicate

query_offset int query_offset()

Returns number of bases consumed from the read sequence.
More concisely,

if current CIGAR operation is 'M', '=', or 'X', index of current read base in the read sequence
if current CIGAR operation is 'D' or 'N', index of read base after the deletion

(in both cases indices are 0-based)

Variables

read Read read;

Meta

Source

See Implementation

bio std hts bam pileup classes

functions

manifest constants

useMD

structs