dhtslib.cigar

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

Members

Enums

Ops
enum Ops

Represents all ops #define BAM_CIGAR_STR "MIDNSHP=XB" #define BAM_CMATCH 0 #define BAM_CINS 1 #define BAM_CDEL 2 #define BAM_CREF_SKIP 3 #define BAM_CSOFT_CLIP 4 #define BAM_CHARD_CLIP 5 #define BAM_CPAD 6 #define BAM_CEQUAL 7 #define BAM_CDIFF 8 #define BAM_CBACK 9

Functions

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)

Structs

AlignedCoordinate
struct AlignedCoordinate

Undocumented in source.

AlignedCoordinatesItr
struct AlignedCoordinatesItr

Undocumented in source.

Cigar
struct Cigar

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

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

Unions

CigarOp
union CigarOp

Represents a distinct cigar operation

Variables

CIGAR_STR
string CIGAR_STR;

Represents all ops #define BAM_CIGAR_STR "MIDNSHP=XB" #define BAM_CMATCH 0 #define BAM_CINS 1 #define BAM_CDEL 2 #define BAM_CREF_SKIP 3 #define BAM_CSOFT_CLIP 4 #define BAM_CHARD_CLIP 5 #define BAM_CPAD 6 #define BAM_CEQUAL 7 #define BAM_CDIFF 8 #define BAM_CBACK 9

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