Namespaces
	missing_values

	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	ChromosomeNotFoundException
	an exception class for the case where a chromosome is not found in the reference More...

class	ChromosomeSizeException
	an exception class for the case where a chromosome is not found in the reference 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	FileOpenException
	Exception for the case where there is an error opening a file for reading/writing. More...

class	Genotype
	Encodes a genotype. More...

class	HeaderCompatibilityException
	Exception for the case where multiple headers are incompatible in some way. More...

class	HeaderReadException
	Exception for the case where a file header could not be read. More...

class	HtslibException
	a catchall exception class for htslib errors More...

class	IndexedSamIterator
	Utility class to enable for-each style iteration in the IndexedSamReader class. More...

class	IndexedSamReader
	Utility class to read a BAM/CRAM file with an appropriate Sam iterator from an indexed file in a for-each loop. Intervals are passed in using a vector of string coordinates compatible with Samtools. When iteration begins, the iterations (re-)starts at the beginning of the first interval. More...

class	IndexedVariantIterator

class	IndexedVariantReader
	Utility class to read an indexed BCF file by intervals using an appropriate Variant iterator in a for-each loop. More...

class	IndexLoadException
	Exception for the case where an index file cannot be opened for a particular file (eg., bam/vcf/bcf) More...

class	IndividualField
	A class template to hold the values of a specific Variant's format field for all samples. More...

class	IndividualFieldIterator
	iterator for VariantField objects. More...

class	IndividualFieldValue
	A class template to hold the values a format field for a particular sample. More...

class	IndividualFieldValueIterator
	iterator for FormatFieldGenericValue objects. More...

class	Interval
	Utility class to store an genomic location (Interval). More...

class	MultipleVariantIterator
	Utility class to enable for-each style iteration in the MultipleVariantReader class. More...

class	MultipleVariantReader
	Utility class to read multiple VCF/BCF files with an appropriate iterator 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	ReadGroup
	Helper struct to hold one read group record from a sam file header. More...

class	ReferenceBlockSplittingVariantIterator
	Utility class to handle reference blocks while iterating over multiple variant files. More...

class	ReferenceIterator
	Utility class to access reference bases in a FastA-formatted reference genome. More...

class	ReferenceMap
	Utility class to create a reference object for all reference operations in Foghorn. More...

class	Sam
	Utility class to manipulate a Sam record. More...

class	SamBuilder
	class to build Sam objects from existing data or from scratch More...

class	SamBuilderDataField
	class to hold encoded byte arrays for individual data fields (cigar, bases, etc.) during building of a Sam 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	SamTag
	class to represent a Sam TAG:TYPE:VALUE entry More...

class	SamWriter
	utility class to write out a SAM/BAM/CRAM file to any stream More...

struct	SharedBufferSpan
	Represents a section (range of bytes) in the shared memory pool VariantBuilderSharedRegion::m_shared_buffer that is currently in use to store encoded field data. More...

class	SharedField
	A class template to hold the values of a specific Variant's shared field. More...

class	SharedFieldIterator
	iterator for SharedField objects. More...

class	SingleInputException
	an exception class for the case where a single input is required, but more is provided More...

class	SyncedVariantIterator
	Utility class to enable for-each style iteration in the SyncedVariantReader class. More...

class	SyncedVariantReader
	Utility class to read multiple VCF.GZ/BCF files with an appropriate iterator in a for-each loop. More...

class	Variant
	Utility class to manipulate a Variant record. More...

class	VariantBuilder
	VariantBuilder: construct Variant records from scratch (and, coming soon, from existing Variant records) More...

class	VariantBuilderCoreField
	Internal VariantBuilder class to represent "core" (non-data-region) fields such as the alignment start and the qual. More...

class	VariantBuilderIndividualField
	Helper class for VariantBuilder to manage the storage and encoding of a single multi-sample individual field. More...

class	VariantBuilderIndividualRegion
	Helper class for VariantBuilder to manage the fields belonging to the individual region of Variant records. More...

class	VariantBuilderMultiSampleVector
	Class that allows you to efficiently prepare multi-sample data for setting individual fields in VariantBuilder. More...

class	VariantBuilderSharedRegion
	Helper class for VariantBuilder to manage the fields belonging to the shared region of Variant records. More...

class	VariantFilters
	class to manipulate filter field objects without making copies. More...

class	VariantFiltersIterator
	simple random-access iterator class for VariantFilters objects More...

class	VariantHeader
	Utility class to hold a variant header. More...

class	VariantHeaderBuilder
	Utility class to build VariantHeader objects from scratch. More...

class	VariantHeaderMerger

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 VCF/BCF file to any stream More...

Typedefs
using	CigarElement = uint32_t

using	IndexedSingleSamReader = IndexedSamReader< IndexedSamIterator >

using	SingleSamReader = SamReader< SamIterator >

using	PairSamReader = SamReader< SamPairIterator >

using	AlleleMask = std::vector< AlleleType >

using	VariantIteratorIndexPair = std::pair< std::shared_ptr< VariantIterator >, uint32_t >

using	VariantIndexPair = std::pair< Variant, uint32_t >

using	InputOrderedVariantHeaderMerger = VariantHeaderMerger< true, true, true, true >

using	FieldOrderedVariantHeaderMerger = VariantHeaderMerger< false, false, false, false >

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...

enum	AlleleType { AlleleType::REFERENCE, AlleleType::SNP, AlleleType::INSERTION, AlleleType::DELETION }

enum	DiploidPLGenotype { DiploidPLGenotype::HOM_REF = 0, DiploidPLGenotype::HET = 1, DiploidPLGenotype::HOM_VAR = 2 }
	simple enum to keep the indices of the genotypes in the PL field of diploid individuals More...

enum	SharedFieldIndex { SharedFieldIndex::ID_INDEX = 0, SharedFieldIndex::REF_ALLELE_INDEX = 1, SharedFieldIndex::ALT_ALLELES_INDEX = 2, SharedFieldIndex::FILTERS_INDEX = 3, SharedFieldIndex::INFO_START_INDEX = 4 }
	Enum to represent the ordering of the various shared fields as they are physically laid out in the encoded data. More...

Functions
void	skip_picard_header (istream &infile)

Interval	parse_interval_record (const string &line)

vector< Interval >	read_intervals (const string &intervals_file)

vector< Interval >	read_intervals (istream &input)

std::vector< Interval >	read_intervals (const std::string &intervals_file)
	utility function to read all Intervals from an Intervals file More...

std::vector< Interval >	read_intervals (std::istream &input)
	utility function to read all Intervals from an Intervals file More...

bool	missing (const bool value)
	Returns true if bool is false (missing). More...

bool	missing (const float value)
	Returns true if float is missing. More...

bool	missing (const int8_t value)
	Returns true if int8_t is missing. More...

bool	missing (const int16_t value)
	Returns true if int16_t is missing. More...

bool	missing (const int32_t value)
	Returns true if int32_t is missing. More...

bool	missing (const std::string &value)
	Returns true if string is missing. More...

bool	missing (const char *value)
	Returns true if char* is missing. More...

template<class MISSING_TYPE >
bool	missing (const MISSING_TYPE &value)

template<class VALUE >
bool	missing (const std::vector< VALUE > &v)

void	subset_variant_samples (bcf_hdr_t *hdr_ptr, const std::vector< std::string > &samples, const bool include)
	allows the caller to include only selected samples in a Variant Reader. To create a sites only file, simply pass an empty vector of samples. More...

void	merge_variant_headers (const std::shared_ptr< bcf_hdr_t > &dest_hdr_ptr, const std::shared_ptr< bcf_hdr_t > &src_hdr_ptr)
	merges a variant header into another More...

Variables
const auto	PICARD_HEADER_TAG = '@'

const auto	sep = char_separator<char>{" \t:-"}

constexpr auto	MATE_CIGAR_TAG = "MC"

Typedef Documentation

using gamgee::AlleleMask = typedef std::vector<AlleleType>

using gamgee::CigarElement = typedef uint32_t

using gamgee::FieldOrderedVariantHeaderMerger = typedef VariantHeaderMerger<false,false,false,false>

using gamgee::IndexedSingleSamReader = typedef IndexedSamReader<IndexedSamIterator>

using gamgee::InputOrderedVariantHeaderMerger = typedef VariantHeaderMerger<true,true,true,true>

using gamgee::PairSamReader = typedef SamReader<SamPairIterator>

using gamgee::SingleSamReader = typedef SamReader<SamIterator>

using gamgee::SingleVariantReader = typedef VariantReader<VariantIterator>

using gamgee::VariantIndexPair = typedef std::pair<Variant, uint32_t>

using gamgee::VariantIteratorIndexPair = typedef std::pair<std::shared_ptr<VariantIterator>, uint32_t>

Enumeration Type Documentation

enum gamgee::AlleleType

strong

Enumerator
REFERENCE
SNP
INSERTION
DELETION

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

enum gamgee::DiploidPLGenotype

strong

simple enum to keep the indices of the genotypes in the PL field of diploid individuals

Enumerator
HOM_REF
HET
HOM_VAR

enum gamgee::SharedFieldIndex

strong

Enum to represent the ordering of the various shared fields as they are physically laid out in the encoded data.

Enumerator
ID_INDEX
REF_ALLELE_INDEX
ALT_ALLELES_INDEX
FILTERS_INDEX
INFO_START_INDEX

Function Documentation

void gamgee::merge_variant_headers	(	const std::shared_ptr< bcf_hdr_t > &	dest_hdr_ptr,
		const std::shared_ptr< bcf_hdr_t > &	src_hdr_ptr
	)

merges a variant header into another

Parameters

dest_hdr_ptr	a shared pointer to a bcf_hdr_t containing the header to be merged into
src_hdr_ptr	a shared pointer to a bcf_hdr_t containing the header to be merged from

bool gamgee::missing ( const bool value )

inline

Returns true if bool is false (missing).

bool gamgee::missing ( const float value )

inline

Returns true if float is missing.

bool gamgee::missing ( const int8_t value )

inline

Returns true if int8_t is missing.

bool gamgee::missing ( const int16_t value )

inline

Returns true if int16_t is missing.

bool gamgee::missing ( const int32_t value )

inline

Returns true if int32_t is missing.

bool gamgee::missing ( const std::string & value )

inline

Returns true if string is missing.

bool gamgee::missing ( const char * value )

inline

Returns true if char* is missing.

template<class MISSING_TYPE >

bool gamgee::missing ( const MISSING_TYPE & value )

inline

Returns true if value is missing.

Template Parameters

MISSING_TYPE any class that implements the missing() as a public member function.

Returns: True if value is missing.

template<class VALUE >

bool gamgee::missing ( const std::vector< VALUE > & v )

inline

Missing overload for functions that return a vector of values. It only applies if the entire vector is missing.

Template Parameters

VALUE any type that can be fit into a container. Any type, really.

Parameters

v	any vector

Returns: true if the vector is empty (therefore the value that was returned is missing)

Interval gamgee::parse_interval_record ( const string & line )

vector<Interval> gamgee::read_intervals ( const string & intervals_file )

vector<Interval> gamgee::read_intervals ( istream & input )

std::vector<Interval> gamgee::read_intervals ( const std::string & intervals_file )

utility function to read all Intervals from an Intervals file

Parameters

intervals_file the file with the Intervals in one of the supported formats

Returns: a vector of Interval objects

std::vector<Interval> gamgee::read_intervals ( std::istream & input )

utility function to read all Intervals from an Intervals file

Parameters

input an input stream (e.g. std::cin)

Returns: a vector of Interval objects

void gamgee::skip_picard_header ( istream & infile )

void gamgee::subset_variant_samples	(	bcf_hdr_t *	hdr_ptr,
		const std::vector< std::string > &	samples,
		const bool	include
	)

allows the caller to include only selected samples in a Variant Reader. To create a sites only file, simply pass an empty vector of samples.

Parameters

samples	the list of samples you want included/excluded from your iteration
whether	you want these samples to be included or excluded from your iteration.

Variable Documentation

constexpr auto gamgee::MATE_CIGAR_TAG = "MC"

const auto gamgee::PICARD_HEADER_TAG = '@'

const auto gamgee::sep = char_separator<char>{" \t:-"}

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation