samtools-0.2.0.1: Binding to the C samtools library

Bio.SamTools.Cigar

Description

Handling of the extended CIGAR pair-wise alignment descriptors

Synopsis

Documentation

data CigarType Source

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

data Cigar Source

Cigar entry including length

Constructors

Cigar 

Fields

cigar :: !CigarType
 
length :: !Int64
 

Instances

toCigar :: CUInt -> CigarSource

Convert a BAM binary cigar integer to a Cigar