dhtslib.sam.cigar

This module simplifies working with CIGAR strings/ops from SAM/BAM/CRAM alignment records.

Members

Ops enum Ops: Represents all cigar ops as a friendlier alternative to BAM_C htslib enums

charToOp Ops charToOp(char c): Convert single char representing a CIGAR Op to Op union
cigarFromString Cigar cigarFromString(string cigar): return Cigar struct for a given CIGAR string (e.g. from SAM line)
isClipping bool isClipping(T op): True iff operation is one of 'S', 'H'
isMatchOrMismatch bool isMatchOrMismatch(T op): True iff operation is one of M, =, X
isQueryConsuming bool isQueryConsuming(T op): True iff operation is one of M, =, X, I, S
isReferenceConsuming bool isReferenceConsuming(T op): True iff operation is one of M, =, X, D, N

CIGAR_STR string CIGAR_STR;: string to aid in conversion from CigarOp to string

AlignedCoordinate struct AlignedCoordinate: Coordinate pair representing aligned query and reference positions, and the CIGAR op at or effecting their alignment.
AlignedCoordinatesItr struct AlignedCoordinatesItr: Iterator yielding all AlignedCoordinate pairs for a given CIGAR string
Cigar struct Cigar: Represents a CIGAR string as an array of CigarOps.
CigarItr struct CigarItr: Range-based iteration of a Cigar string Returns a range of Ops that is the length of all op lengths e.g. if the Cigar is 4M5D2I4M CigarItr will return a range of MMMMDDDDDIIMMMM Range is of the Ops enum not chars