Cigar

Represents a CIGAR string as an array of CigarOps.

https://samtools.github.io/hts-specs/SAMv1.pdf §1.4.6

In many cases will represent a slice or reference to underlying cigar data in the bam record UNLESS it is copied with .dup or one of the assignment methods.

Constructors

this this(Bam1 b): Construct Cigar from SAMRecord
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 deprecated alias ref_bases_covered = refBasesCovered: Undocumented in source.

Functions

dup auto dup(): copy cigar
is_null bool is_null(): null CIGAR -- don't read!
length auto length(): get length of cigar
length void length(T len): set length of cigar
opApply int opApply(int delegate(ref CigarOp) dg): allow foreach on Cigar
opAssign auto opAssign(T value): Assign a Cigar with a Cigar Note: this is not a deep copy
opAssign auto opAssign(T value): Assign a Cigar with a CigarOp slice Note: this is not a deep copy
opBinary auto opBinary(Cigar rhs): combine Cigars
opDollar size_t opDollar(): use $ with Cigar slicing
opIndex auto ref opIndex(ulong i): Get a cigar op from a single position in the Cigar string
opIndexAssign auto opIndexAssign(CigarOp value, size_t index): Assign a cigar op at a single position in the Cigar string
opSlice auto opSlice(): Get a Slice of cigar ops from a range in the Cigar string
opSlice auto opSlice(T start, T end): Get a Slice of cigar ops from a range in the Cigar string
opSliceAssign auto opSliceAssign(CigarOp[] values, T start, T end): Assign a range cigar ops over a range in the Cigar string
toString string toString(): Format Cigar struct as CIGAR string in accordance with SAM spec

Properties

refBasesCovered int refBasesCovered [@property getter]: return the alignment length expressed by this Cigar