Cigar

Represents a CIGAR string https://samtools.github.io/hts-specs/SAMv1.pdf §1.4.6

struct Cigar {

CigarOp[] ops;

this(uint* cigar, uint length);

this(CigarOp[] ops);

bool is_null();

string toString();

int refBasesCovered();

alias ref_bases_covered = refBasesCovered;

alias alignedLength = refBasesCovered;

}

Constructors

this this(uint* cigar, uint length): Construct Cigar from raw data
this this(CigarOp[] ops): Construct Cigar from an array of CIGAR ops

Members

Aliases

alignedLength alias alignedLength = refBasesCovered: previous alignedLength function had a bug and it is just a duplicate of ref_bases_covered
ref_bases_covered alias ref_bases_covered = refBasesCovered: Undocumented in source.

Functions

is_null bool is_null(): Undocumented in source. Be warned that the author may not have intended to support it.
refBasesCovered int refBasesCovered(): return the alignment length expressed by this Cigar TODO: use CIGAR_TYPE to get rid of switch statement for less branching
toString string toString(): Format Cigar struct as CIGAR string in accordance with SAM spec

Variables

ops CigarOp[] ops;: array of distinct CIGAR ops

Meta

Source

See Implementation

dhtslib cigar enums

Ops

functions

structs

unions

CigarOp

variables

CIGAR_STR