utility functions for the gamgee library More...

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

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...

Functions
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...

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...

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...

template<typename T , typename... Args>
std::unique_ptr< T >	make_unique (Args &&...args)
	herb sutter's implementation of make unique 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...

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

Function Documentation

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 )

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::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< 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

template<typename T , typename... Args>

std::unique_ptr< T > gamgee::utils::make_unique ( Args &&... args )

herb sutter's implementation of make unique

Note: this is going to become standard in C++14, we can drop this as soon as gcc 4.9 and clang 3.5 are released

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

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

Classes

Functions

Detailed Description

Function Documentation