gamgee Namespace Reference

Namespaces
	utils
	utility functions for the gamgee library

Classes
class	BaseQuals
	Utility class to handle the memory management of the sam record object for a read base qualities. More...
class	Cigar
	Utility class to manage the memory of the cigar structure. More...
class	Fastq
	Utility class to hold one FastA or FastQ record. More...
class	FastqIterator
	Utility class to enable for-each style iteration in the FastqReader class. More...
class	FastqReader
	Utility class to read many Fastq records from a stream (e.g. Fastq file, stdin, ...) in a for-each loop in a for-each loop. More...
class	ReadBases
	Utility class to handle the memory management of the sam record object for read bases. More...
class	Sam
	Utility class to manipulate a Sam record. More...
class	SamHeader
	Utility class to hold the header of a sam file. More...
class	SamIterator
	Utility class to enable for-each style iteration in the SamReader class. More...
class	SamPairIterator
	Utility class to enable for-each style iteration by pairs in the SamReader class. More...
class	SamReader
	Utility class to read a SAM/BAM/CRAM file with an appropriate Sam iterator from a stream (e.g. file, stdin, ...) in a for-each loop. More...
class	SamWriter
	utility class to write out a SAM/BAM/CRAM file to any stream More...
class	Variant
	Utility class to manipulate a Variant record. More...
class	VariantHeader
	Utility class to hold a variant header. More...
class	VariantHeaderBuilder
	Utility class to build VariantHeader objects from scratch. More...
class	VariantIterator
	Utility class to enable for-each style iteration in the VariantReader class. More...
class	VariantReader
	Utility class to read a VCF/BCF file with an appropriate Variant iterator from a stream (e.g. file, stdin, ...) in a for-each loop. More...
class	VariantWriter
	utility class to write out a SAM/BAM/CRAM file to any stream More...

Typedefs
using	SingleSamReader = SamReader< SamIterator >
using	PairSamReader = SamReader< SamPairIterator >
using	SingleVariantReader = VariantReader< VariantIterator >

Enumerations
enum	CigarOperator {   CigarOperator::M, CigarOperator::I, CigarOperator::D, CigarOperator::N,   CigarOperator::S, CigarOperator::H, CigarOperator::P, CigarOperator::EQ,   CigarOperator::X, CigarOperator::B }
	comprehensive list of valid cigar operators More...
enum	Base {   Base::A = 1, Base::C = 2, Base::G = 4, Base::T = 8,   Base::N = 15 }
	simple enum to hold all valid bases in the SAM format More...

Typedef Documentation

using gamgee::PairSamReader = typedef SamReader<SamPairIterator>

using gamgee::SingleSamReader = typedef SamReader<SamIterator>

using gamgee::SingleVariantReader = typedef VariantReader<VariantIterator>

Enumeration Type Documentation

enum gamgee::Base

strong

simple enum to hold all valid bases in the SAM format

Note

enum values used here correspond to the 4-bit base encodings in htslib so that we can cast directly to Base

Enumerator
A
C
G
T
N

enum gamgee::CigarOperator

strong

comprehensive list of valid cigar operators

Note

order of the operators in this enum must match the order in BAM_CIGAR_STR from htslib/sam.h

Enumerator
M
I
D
N
S
H
P
EQ
X
B