utility functions for the gamgee library More...

Classes
struct	HtsFileDeleter
	a functor object to delete an htsFile pointer More...

struct	HtsIndexDeleter
	a functor object to delete an hts file index pointer More...

struct	HtsIteratorDeleter
	a functor object to delete an hts file iterator pointer More...

struct	IFStreamDeleter
	a functor object to delete an ifstream More...

class	MergedVCFAllelesIdxLUT
	LUT class for storing mappings between allele vectors in the merged file and input VCF files Since the #alleles per site is expected to be small, this class sets the number of fields to 10. This makes any subsequent re-allocations unlikely. The function resize_luts_if_needed() will almost always return immediately after failing the if condition. More...

class	MergedVCFLUTBase
	Base class to store look up information between fields of merged header and input headers. More...

struct	SamBodyDeleter
	a functor object to delete a bam1_t pointer More...

struct	SamHeaderDeleter
	a functor object to delete a bam_hdr_t pointer More...

class	ShortValueOptimizedStorage

struct	SyncedReaderDeleter
	a functor object to delete a bcf_srs_t pointer More...

struct	VariantBodyDeleter
	a functor object to delete a bcf1_t pointer More...

struct	VariantHeaderDeleter
	a functor object to delete a bcf_hdr_t pointer More...

Typedefs
using	CombineAllelesLUT = MergedVCFAllelesIdxLUT< true, true >

Enumerations
enum	VariantFieldType { VariantFieldType::NIL = 0, VariantFieldType::INT8 = 1, VariantFieldType::INT16 = 2, VariantFieldType::INT32 = 3, VariantFieldType::FLOAT = 5, VariantFieldType::STRING = 7 }
	an enumeration of the types in htslib for the format field values More...

Functions
std::shared_ptr< std::ifstream >	make_shared_ifstream (std::ifstream *ifstream_ptr)
	wraps a pre-allocated ifstream in a shared_ptr with correct deleter More...

std::shared_ptr< std::ifstream >	make_shared_ifstream (std::string filename)
	wraps an input file in a shared_ptr to an ifstream with correct deleter More...

template<class TYPE >
bool	allele_missing (const uint8_t *data_ptr, const uint32_t allele_index, const TYPE missing)

template<class TYPE >
vector< int32_t >	allele_keys (const std::shared_ptr< bcf1_t > &body, const bcf_fmt_t const format_ptr, const uint8_t data_ptr, const TYPE missing, const TYPE vector_end)

template<class TYPE >
vector< string >	allele_strings (const std::shared_ptr< bcf1_t > &body, const bcf_fmt_t const format_ptr, const uint8_t data_ptr, const TYPE missing, const TYPE vector_end)

bool	allele_missing (const bcf_fmt_t const format_ptr, const uint8_t data_ptr, const uint32_t allele_index)
	Returns true if the allele at position allele_index is missing. More...

vector< int32_t >	allele_keys (const std::shared_ptr< bcf1_t > &body, const bcf_fmt_t const format_ptr, const uint8_t data_ptr)
	Returns the genotype allele keys. More...

vector< string >	allele_strings (const std::shared_ptr< bcf1_t > &body, const bcf_fmt_t const format_ptr, const uint8_t data_ptr)
	Returns the genotype allele strings. More...

string	allele_key_to_string (const std::shared_ptr< bcf1_t > &body, const int32_t key_index)
	Returns the genotype allele string from this line. More...

uint32_t	allele_count (const bcf_fmt_t *const format_ptr)
	Counts the genotype alleles. More...

template<class TYPE >
int32_t	allele_key (const uint8_t *data_ptr, const uint32_t allele_index, const TYPE missing, const TYPE vector_end)

int32_t	allele_key (const bcf_fmt_t const format_ptr, const uint8_t data_ptr, const uint32_t allele_index)
	Returns the genotype allele at position allele_index. More...

shared_ptr< htsFile >	make_shared_hts_file (htsFile *hts_file_ptr)
	wraps a pre-allocated htsFile in a shared_ptr with correct deleter More...

shared_ptr< hts_idx_t >	make_shared_hts_index (hts_idx_t *hts_index_ptr)
	wraps a pre-allocated hts_idx_t in a shared_ptr with correct deleter More...

shared_ptr< hts_itr_t >	make_shared_hts_itr (hts_itr_t *hts_itr_ptr)
	wraps a pre-allocated hts_itr_t in a shared_ptr with correct deleter More...

shared_ptr< bam1_t >	make_shared_sam (bam1_t *sam_ptr)
	wraps a pre-allocated bam1_t in a shared_ptr with correct deleter More...

shared_ptr< bam_hdr_t >	make_shared_sam_header (bam_hdr_t *sam_header_ptr)
	wraps a pre-allocated bam_hdr_t in a shared_ptr with correct deleter More...

shared_ptr< bcf1_t >	make_shared_variant (bcf1_t *bcf_ptr)
	wraps a pre-allocated bcf1_t in a shared_ptr with correct deleter More...

shared_ptr< bcf_hdr_t >	make_shared_variant_header (bcf_hdr_t *bcf_hdr_ptr)
	wraps a pre-allocated bcf_hdr_t in a shared_ptr with correct deleter More...

std::shared_ptr< bcf_srs_t >	make_shared_synced_variant_reader (bcf_srs_t *synced_reader_ptr)
	wraps a pre-allocated bcf_srs_t in a shared_ptr with correct deleter More...

unique_ptr< htsFile, HtsFileDeleter >	make_unique_hts_file (htsFile *hts_file_ptr)
	wraps a pre-allocated htsFile in a unique_ptr with correct deleter More...

std::unique_ptr< hts_itr_t, HtsIteratorDeleter >	make_unique_hts_itr (hts_itr_t *hts_itr_ptr)
	wraps a pre-allocated hts_itr_t in a unique_ptr with correct deleter More...

bam1_t *	sam_deep_copy (bam1_t *original)
	creates a deep copy of an existing bam1_t More...

bam_hdr_t *	sam_header_deep_copy (bam_hdr_t *original)
	creates a deep copy of an existing bam_hdr_t More...

bcf1_t *	variant_deep_copy (bcf1_t *original)
	creates a deep copy of an existing bcf1_t More...

bcf_hdr_t *	variant_header_deep_copy (bcf_hdr_t *original)
	creates a deep copy of an existing bcf_hdr_t More...

bam1_t *	sam_shallow_copy (bam1_t *original)
	creates a shallow copy of an existing bam1_t: copies core fields but not the data buffer or fields related to the size of the data buffer More...

std::string	htslib_filter_name (bcf_hdr_t header, bcf1_t body, int index)
	helper function to translate an index into a string in the filter list More...

uint8_t	bcf_type_to_element_size (const int32_t htslib_type)
	Returns the number of bytes required to store each BCF_BT_* type. More...

uint8_t	int_encoded_type (const int32_t min_val, const int32_t max_val)
	Given a min and max value, determines whether int8, int16, or int32 BCF encoding is required. More...

kstring_t	initialize_htslib_buffer (const uint32_t initial_capacity)
	Returns a newly-allocated kstring_t buffer suitable for passing to htslib. More...

uint8_t	int_encoded_type (const int32_t val)

uint8_t	int_encoded_size (const int32_t val)

uint32_t	encoded_size (const int8_t field_type, const uint32_t field_length, bool add_type_descriptor=true)

char	complement_base (const char base)

std::string	complement (std::string &sequence)
	calculates the complement of a sequence in-place More...

std::string	complement (const std::string &sequence)
	calculates the complement of a sequence More...

std::string	reverse_complement (const std::string &sequence)
	calculates the reverse complement of a sequence More...

std::vector< std::string >	hts_string_array_to_vector (const char const const string_array, const uint32_t array_size)
	converts an array of c-strings into a vector<string> More...

char	complement (const char base)
	calculates the complement of a base More...

void	check_max_boundary (const uint32_t index, const uint32_t size, const std::string &prefix_msg)
	checks that an index is greater than or equal to size More...

void	check_max_boundary (const uint32_t index, const uint32_t size)
	checks that an index is greater than or equal to size More...

template<class TYPE >
bool	bcf_check_equal_element (const TYPE &x, const TYPE &y)
	Check whether two values from VCF fields of primitive types (for which the == operator is defined) * are equal The function template is specialized for float fields More...

template<>
bool	bcf_check_equal_element< float > (const float &x, const float &y)
	: Check whether two float values from VCF fields are equal More...

template<class TYPE >
bool	bcf_is_vector_end_value (const TYPE &value)

template<>
bool	bcf_is_vector_end_value< int32_t > (const int32_t &value)

template<>
bool	bcf_is_vector_end_value< float > (const float &value)

template<class ITER >
const uint8_t *	cache_and_advance_to_end_if_necessary (const uint8_t current_ptr, const uint8_t end_ptr, ITER &it)
	advances current ptr to end of the vector if the current element is bcf_*_vector_end More...

int32_t	convert_data_to_integer (const uint8_t *data_ptr, const int index, const uint8_t num_bytes_per_value, const VariantFieldType &type)
	converts the value in an index from the byte array into int32_t More...

float	convert_data_to_float (const uint8_t *data_ptr, const int index, const uint8_t num_bytes_per_value, const VariantFieldType &type)
	converts the value in an index from the byte array into float More...

std::string	convert_data_to_string (const uint8_t *data_ptr, const int index, const uint8_t num_bytes_per_value, const VariantFieldType &type)
	converts the value in an index from the byte array into string More...

uint8_t	size_for_type (const VariantFieldType &type, const bcf_fmt_t *const format_ptr)
	returns the number of bytes for a given VariantFieldType More...

uint8_t	size_for_type (const VariantFieldType &type, const bcf_info_t *const info_ptr)
	returns the number of bytes for a given VariantFieldType More...

bool	is_string_type (const int32_t &type)
	check if type is of type string More...

template<typename... T>
auto	zip (const T &...containers) -> boost::iterator_range< boost::zip_iterator< decltype(boost::make_tuple(containers.begin()...))>>
	utility method to zip iterators together with simpler syntax than boost More...

Variables
const uint8_t	bcf_type_sizes [] = { 0, 1, 2, 4, 0, 4, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0 }

Detailed Description

utility functions for the gamgee library

This namespace includes typical functors and templates for DNA sequence manipulation as well as low level routines for htslib memory management

Typedef Documentation

using gamgee::utils::CombineAllelesLUT = typedef MergedVCFAllelesIdxLUT<true,true>

Enumeration Type Documentation

enum gamgee::utils::VariantFieldType

strong

an enumeration of the types in htslib for the format field values

Note: these must match the order in the htslib defines in htslib/vcf.h

Enumerator
NIL
INT8
INT16
INT32
FLOAT
STRING

Function Documentation

uint32_t gamgee::utils::allele_count ( const bcf_fmt_t *const format_ptr )

inline

Counts the genotype alleles.

Parameters

format_ptr The GT field from the line.

Returns: the count of genotype alleles.

Warning: format_ptr must be non-null.

template<class TYPE >

int32_t gamgee::utils::allele_key	(	const uint8_t *	data_ptr,
		const uint32_t	allele_index,
		const TYPE	missing,
		const TYPE	vector_end
	)

inline

int32_t gamgee::utils::allele_key	(	const bcf_fmt_t *const	format_ptr,
		const uint8_t *	data_ptr,
		const uint32_t	allele_index
	)

inline

Returns the genotype allele at position allele_index.

Parameters

format_ptr	The GT field from the line.
data_ptr	The GT for this sample.
allele_index	The index within the GT field to return an integer allele.

Returns: The genotype allele at position allele_index.

Warning: Only int8_t GT fields have been tested.

string gamgee::utils::allele_key_to_string	(	const std::shared_ptr< bcf1_t > &	body,
		const int32_t	key_index
	)

Returns the genotype allele string from this line.

Parameters

body	The shared memory variant "line" from a vcf, or bcf.
key_index	The integer representation of the allele within this "line".

Returns: The genotype allele string from this line.

Warning: Only int8_t GT fields have been tested.

template<class TYPE >

vector< int32_t > gamgee::utils::allele_keys	(	const std::shared_ptr< bcf1_t > &	body,
		const bcf_fmt_t *const	format_ptr,
		const uint8_t *	data_ptr,
		const TYPE	missing,
		const TYPE	vector_end
	)

vector< int32_t > gamgee::utils::allele_keys	(	const std::shared_ptr< bcf1_t > &	body,
		const bcf_fmt_t *const	format_ptr,
		const uint8_t *	data_ptr
	)

Returns the genotype allele keys.

Parameters

body	The shared memory variant "line" from a vcf, or bcf.
format_ptr	The GT field from the line.
data_ptr	The GT for this sample.

Returns: The genotype allele keys.

Warning: Only int8_t GT fields have been tested.

template<class TYPE >

bool gamgee::utils::allele_missing	(	const uint8_t *	data_ptr,
		const uint32_t	allele_index,
		const TYPE	missing
	)

bool gamgee::utils::allele_missing	(	const bcf_fmt_t *const	format_ptr,
		const uint8_t *	data_ptr,
		const uint32_t	allele_index
	)

Returns true if the allele at position allele_index is missing.

Parameters

format_ptr	The GT field from the line.
data_ptr	The GT for this sample.
allele_index	The index within the GT field to return an integer allele.

Returns: true if the allele at position allele_index is missing.

Warning: Only int8_t GT fields have been tested.; Missing GT fields are untested.

template<class TYPE >

vector< string > gamgee::utils::allele_strings	(	const std::shared_ptr< bcf1_t > &	body,
		const bcf_fmt_t *const	format_ptr,
		const uint8_t *	data_ptr,
		const TYPE	missing,
		const TYPE	vector_end
	)

vector< string > gamgee::utils::allele_strings	(	const std::shared_ptr< bcf1_t > &	body,
		const bcf_fmt_t *const	format_ptr,
		const uint8_t *	data_ptr
	)

Returns the genotype allele strings.

Parameters

body	The shared memory variant "line" from a vcf, or bcf.
format_ptr	The GT field from the line.
data_ptr	The GT for this sample.

Returns: The genotype allele strings.

Warning: Only int8_t GT fields have been tested.

template<class TYPE >

bool gamgee::utils::bcf_check_equal_element	(	const TYPE &	x,
		const TYPE &	y
	)

inline

Check whether two values from VCF fields of primitive types (for which the == operator is defined) * are equal The function template is specialized for float fields

template<>

bool gamgee::utils::bcf_check_equal_element< float >	(	const float &	x,
		const float &	y
	)

inline

: Check whether two float values from VCF fields are equal

Note: : since bcf_float_missing and bcf_float_vector_end are represented as NaNs and (nan == nan) returns false, a special check needs to be done for checking equality of float values in VCFs

template<class TYPE >

bool gamgee::utils::bcf_is_vector_end_value ( const TYPE & value )

inline

template<>

bool gamgee::utils::bcf_is_vector_end_value< float > ( const float & value )

inline

template<>

bool gamgee::utils::bcf_is_vector_end_value< int32_t > ( const int32_t & value )

inline

uint8_t gamgee::utils::bcf_type_to_element_size ( const int32_t htslib_type )

Returns the number of bytes required to store each BCF_BT_* type.

template<class ITER >

const uint8_t* gamgee::utils::cache_and_advance_to_end_if_necessary	(	const uint8_t *	current_ptr,
		const uint8_t *	end_ptr,
		ITER &	it
	)

inline

advances current ptr to end of the vector if the current element is bcf_*_vector_end

void gamgee::utils::check_max_boundary	(	const uint32_t	index,
		const uint32_t	size,
		const std::string &	prefix_msg
	)

inline

checks that an index is greater than or equal to size

Parameters

index	the index between 0 and size to check
size	one past the maximum valid index
prefix_msg	additional string to prefix error message

Exceptions

throws an out_of_bounds exception if index is out of limits

<

Todo:: update this to auto when gcc-4.9 is available on travis-ci

void gamgee::utils::check_max_boundary	(	const uint32_t	index,
		const uint32_t	size
	)

inline

checks that an index is greater than or equal to size

Parameters

index	the index between 0 and size to check
size	one past the maximum valid index

Exceptions

throws an out_of_bounds exception if index is out of limits

std::string gamgee::utils::complement ( std::string & sequence )

calculates the complement of a sequence in-place

Parameters

sequence the sequence to turn into the complement

Returns: the complement of the sequence calculated in-place (modifies the sequence)

std::string gamgee::utils::complement ( const std::string & sequence )

calculates the complement of a sequence

Parameters

sequence the sequence to get the complement from

Returns: a new string with the complement of the sequence

char gamgee::utils::complement ( const char base )

calculates the complement of a base

Parameters

base	the base to get the complement from

Returns: a new char with the complement of base

char gamgee::utils::complement_base ( const char base )

float gamgee::utils::convert_data_to_float	(	const uint8_t *	data_ptr,
		const int	index,
		const uint8_t	num_bytes_per_value,
		const VariantFieldType &	type
	)

converts the value in an index from the byte array into float

int32_t gamgee::utils::convert_data_to_integer	(	const uint8_t *	data_ptr,
		const int	index,
		const uint8_t	num_bytes_per_value,
		const VariantFieldType &	type
	)

converts the value in an index from the byte array into int32_t

The byte array's underlying data representation is record specific, meaning that even numbers (like Integer) can be represented multiple ways across registers (some with uint8_t others with uint32_t...) dictated by the the maximum value in the field.

This member function provides correct index location and appropriately creates a new value of VALUE_TYPE to return to the user.

Exceptions

Will	throw std::invalid_argument exception if trying to create a string out of a numeric format or vice-versa. All numeric type conversions are internally truncated or expanded accordingly.

std::string gamgee::utils::convert_data_to_string	(	const uint8_t *	data_ptr,
		const int	index,
		const uint8_t	num_bytes_per_value,
		const VariantFieldType &	type
	)

converts the value in an index from the byte array into string

uint32_t gamgee::utils::encoded_size	(	const int8_t	field_type,
		const uint32_t	field_length,
		bool	add_type_descriptor = `true`
	)

inline

std::vector< std::string > gamgee::utils::hts_string_array_to_vector	(	const char const const	string_array,
		const uint32_t	array_size
	)

converts an array of c-strings into a vector<string>

Useful in many hts structs where a list of names is stored as a char** and we want to manipulate it in a vector<string> to maintain data contiguity and improve usability

std::string gamgee::utils::htslib_filter_name	(	bcf_hdr_t *	header,
		bcf1_t *	body,
		int	index
	)

helper function to translate an index into a string in the filter list

Parameters

header	a VariantHeader htslib pointer
body	a Variant htslib pointer
index	the index of the filter you want access to

kstring_t gamgee::utils::initialize_htslib_buffer ( const uint32_t initial_capacity )

Returns a newly-allocated kstring_t buffer suitable for passing to htslib.

The returned buffer is safe for htslib to call realloc() on, since it is initially allocated with malloc().

Warning: Use this function ONLY when the memory will be handled to htslib for management and eventual release (eg., copying the buffer pointer into a bcf1_t) – it is the caller's responsibility to make sure deallocation is taken care of.

uint8_t gamgee::utils::int_encoded_size ( const int32_t val )

inline

uint8_t gamgee::utils::int_encoded_type ( const int32_t val )

inline

uint8_t gamgee::utils::int_encoded_type	(	const int32_t	min_val,
		const int32_t	max_val
	)

Given a min and max value, determines whether int8, int16, or int32 BCF encoding is required.

bool gamgee::utils::is_string_type ( const int32_t & type )

inline

check if type is of type string

std::shared_ptr< htsFile > gamgee::utils::make_shared_hts_file ( htsFile * hts_file_ptr )

wraps a pre-allocated htsFile in a shared_ptr with correct deleter

Parameters

hts_file_ptr an htslib raw file pointer

std::shared_ptr< hts_idx_t > gamgee::utils::make_shared_hts_index ( hts_idx_t * hts_index_ptr )

wraps a pre-allocated hts_idx_t in a shared_ptr with correct deleter

Parameters

hts_index_ptr an htslib raw file index pointer

std::shared_ptr< hts_itr_t > gamgee::utils::make_shared_hts_itr ( hts_itr_t * hts_itr_ptr )

wraps a pre-allocated hts_itr_t in a shared_ptr with correct deleter

Parameters

hts_itr_ptr an htslib raw file iterator pointer

std::shared_ptr< std::ifstream > gamgee::utils::make_shared_ifstream ( std::ifstream * ifstream_ptr )

wraps a pre-allocated ifstream in a shared_ptr with correct deleter

Parameters

ifstream_ptr an ifstream raw file pointer

std::shared_ptr< std::ifstream > gamgee::utils::make_shared_ifstream ( std::string filename )

wraps an input file in a shared_ptr to an ifstream with correct deleter

Parameters

filename the input filename

std::shared_ptr< bam1_t > gamgee::utils::make_shared_sam ( bam1_t * sam_ptr )

wraps a pre-allocated bam1_t in a shared_ptr with correct deleter

Parameters

sam_ptr an htslib raw bam pointer

std::shared_ptr< bam_hdr_t > gamgee::utils::make_shared_sam_header ( bam_hdr_t * sam_header_ptr )

wraps a pre-allocated bam_hdr_t in a shared_ptr with correct deleter

Parameters

sam_header_ptr an htslib raw bam header pointer

std::shared_ptr< bcf_srs_t > gamgee::utils::make_shared_synced_variant_reader ( bcf_srs_t * synced_reader_ptr )

wraps a pre-allocated bcf_srs_t in a shared_ptr with correct deleter

Parameters

synced_reader_ptr an htslib synced BCF reader pointer

std::shared_ptr< bcf1_t > gamgee::utils::make_shared_variant ( bcf1_t * bcf_ptr )

wraps a pre-allocated bcf1_t in a shared_ptr with correct deleter

Parameters

bcf_ptr an htslib raw vcf pointer

std::shared_ptr< bcf_hdr_t > gamgee::utils::make_shared_variant_header ( bcf_hdr_t * bcf_hdr_ptr )

wraps a pre-allocated bcf_hdr_t in a shared_ptr with correct deleter

Parameters

bcf_hdr_ptr an htslib raw variant header pointer

std::unique_ptr< htsFile, HtsFileDeleter > gamgee::utils::make_unique_hts_file ( htsFile * hts_file_ptr )

wraps a pre-allocated htsFile in a unique_ptr with correct deleter

Parameters

hts_file_ptr an htslib raw file pointer

std::unique_ptr< hts_itr_t, HtsIteratorDeleter > gamgee::utils::make_unique_hts_itr ( hts_itr_t * hts_itr_ptr )

wraps a pre-allocated hts_itr_t in a unique_ptr with correct deleter

Parameters

hts_itr_ptr an htslib raw file iterator pointer

std::string gamgee::utils::reverse_complement ( const std::string & sequence )

calculates the reverse complement of a sequence

Parameters

sequence the sequence to get the reverse complement from

Returns: a new string with the reverse complement of the sequence

bam1_t * gamgee::utils::sam_deep_copy ( bam1_t * original )

creates a deep copy of an existing bam1_t

Parameters

original an htslib raw bam pointer

bam_hdr_t * gamgee::utils::sam_header_deep_copy ( bam_hdr_t * original )

creates a deep copy of an existing bam_hdr_t

Parameters

original an htslib raw bam header pointer

bam1_t * gamgee::utils::sam_shallow_copy ( bam1_t * original )

creates a shallow copy of an existing bam1_t: copies core fields but not the data buffer or fields related to the size of the data buffer

uint8_t gamgee::utils::size_for_type	(	const VariantFieldType &	type,
		const bcf_fmt_t *const	format_ptr
	)

returns the number of bytes for a given VariantFieldType

uint8_t gamgee::utils::size_for_type	(	const VariantFieldType &	type,
		const bcf_info_t *const	info_ptr
	)

returns the number of bytes for a given VariantFieldType

bcf1_t * gamgee::utils::variant_deep_copy ( bcf1_t * original )

creates a deep copy of an existing bcf1_t

Parameters

original an htslib raw bcf pointer

bcf_hdr_t * gamgee::utils::variant_header_deep_copy ( bcf_hdr_t * original )

creates a deep copy of an existing bcf_hdr_t

Parameters

original an htslib raw bcf header pointer

template<typename... T>

auto gamgee::utils::zip ( const T &... containers ) -> boost::iterator_range<boost::zip_iterator<decltype(boost::make_tuple(containers.begin()...))>>

utility method to zip iterators together with simpler syntax than boost

This is a wrapper over boost's zip_iterator interface to simplify the usage of zip iterators especially in for each loops. This function enables the following syntax:

for (const auto tup : zip(a, b, c, d) {
  ... // use tup values as a boost::tuple
}

for more details look at boost's zip_iterator documentation.

Variable Documentation

const uint8_t gamgee::utils::bcf_type_sizes[] = { 0, 1, 2, 4, 0, 4, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0 }

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