Bio.SamTools.Cigar

Handling of the extended CIGAR pair-wise alignment descriptors

Documentation

data CigarType

Cigar entry types

Constructors

Match

Aligned nucleotide, may be a match or mismatch

Ins

Insertion in read relative to reference

Del

Deletion from read relative to reference

RefSkip

Skipped reference bases, i.e., splice

SoftClip

Trimmed nucleotides, still present in read

HardClip

Trimmed nucleotides, removed from read

Pad

Deletion from padded reference

Instances

Bounded CigarType

Enum CigarType

Eq CigarType

Ord CigarType

Show CigarType

data Cigar

Cigar entry including length

Constructors

Cigar

Fields

cigar :: !CigarType

length :: !Int64

Instances

Eq Cigar

Ord Cigar

Show Cigar

toCigar :: CUInt -> Cigar

Convert a BAM binary cigar integer to a Cigar

cigarToSpLoc :: Int64 -> [Cigar] -> SpliceLoc

cigarToAlignment :: Int64 -> [Cigar] -> [(Maybe Pos, Maybe Pos)]