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

#include <variant_builder_multi_sample_vector.h>

Public Member Functions
	VariantBuilderMultiSampleVector (const uint32_t num_samples, const uint32_t max_values_per_sample, const ELEMENT_TYPE missing_value, const ELEMENT_TYPE end_of_vector_value)
	Construct a VariantBuilderMultiSampleVector. More...

	VariantBuilderMultiSampleVector (const VariantBuilderMultiSampleVector &other)=default

VariantBuilderMultiSampleVector &	operator= (const VariantBuilderMultiSampleVector &other)=default

	VariantBuilderMultiSampleVector (VariantBuilderMultiSampleVector &&other)=default

VariantBuilderMultiSampleVector &	operator= (VariantBuilderMultiSampleVector &&other)=default

	~VariantBuilderMultiSampleVector ()=default

void	set_sample_value (const uint32_t sample_index, const uint32_t value_index, const ELEMENT_TYPE value)
	Set a single value for one sample. More...

void	set_sample_values (const uint32_t sample_index, const std::vector< ELEMENT_TYPE > &values)
	Set all values for one sample at once. More...

const std::vector< ELEMENT_TYPE > &	get_vector () const
	Get a reference to the internal one-dimensional vector used for value storage. More...

uint32_t	num_samples () const
	Return the number of samples whose values we are storing. More...

uint32_t	max_values_per_sample () const
	Return the maximum number of values across all samples. More...

Friends
class	VariantBuilder

Detailed Description

template<class ELEMENT_TYPE>
class gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >

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

For those who want higher performance than is possible with the vector<vector> individual field setters in VariantBuilder, this class is available as an alternative. Internally it uses a flattened, pre-padded one-dimensional vector that can be passed directly to htslib for encoding, and so has much better data locality and cache performance than a two-dimensional vector.

To use, first determine the number of samples and the maximum number of values per sample for the field. Then get a pre-initialized VariantBuilderMultiSampleVector from your VariantBuilder instance. Eg.,

auto multi_sample_vector = builder.get_integer_multi_sample_vector(num_samples, max_values_per_sample);

(NOTE: DO NOT INSTANTIATE THIS CLASS DIRECTLY! ALWAYS GET AN INSTANCE FROM A VARIANTBUILDER OBJECT)

This multi_sample_vector will have missing values for all samples, with appropriate padding to the maximum field width.

Then, fill in the values for each non-missing sample by invoking the set_sample_value() and/or set_sample_values() functions on your multi-sample vector (NOTE: set_sample_value() is MUCH more efficient than set_sample_values() since it doesn't require a vector construction/destruction for each call). You don't have to worry about samples with no values, since all samples start out with missing values.

Finally, pass your multi-sample vector into a VariantBuilder setter function (favoring the functions that take field indices and use move semantics for high performance). Eg.,

builder.set_integer_individual_field(field_index, std::move(multi_sample_vector));

Constructor & Destructor Documentation

template<class ELEMENT_TYPE>

gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::VariantBuilderMultiSampleVector	(	const uint32_t	num_samples,
		const uint32_t	max_values_per_sample,
		const ELEMENT_TYPE	missing_value,
		const ELEMENT_TYPE	end_of_vector_value
	)

inline

Construct a VariantBuilderMultiSampleVector.

Parameters

num_samples	number of samples we will be storing in this vector
max_values_per_sample	maximum number of values across all samples
missing_value	the BCF missing value for this type
end_of_vector_value	the BCF end of vector value for this type

Note: : DO NOT INSTANTIATE THIS CLASS DIRECTLY! ALWAYS GET AN INSTANCE FROM A VARIANTBUILDER OBJECT

template<class ELEMENT_TYPE>

gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::VariantBuilderMultiSampleVector ( const VariantBuilderMultiSampleVector< ELEMENT_TYPE > & other )

default

template<class ELEMENT_TYPE>

gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::VariantBuilderMultiSampleVector ( VariantBuilderMultiSampleVector< ELEMENT_TYPE > && other )

default

template<class ELEMENT_TYPE>

gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::~VariantBuilderMultiSampleVector ( )

default

Member Function Documentation

template<class ELEMENT_TYPE>

const std::vector<ELEMENT_TYPE>& gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::get_vector ( ) const

inline

Get a reference to the internal one-dimensional vector used for value storage.

template<class ELEMENT_TYPE>

uint32_t gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::max_values_per_sample ( ) const

inline

Return the maximum number of values across all samples.

template<class ELEMENT_TYPE>

uint32_t gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::num_samples ( ) const

inline

Return the number of samples whose values we are storing.

template<class ELEMENT_TYPE>

VariantBuilderMultiSampleVector& gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::operator= ( const VariantBuilderMultiSampleVector< ELEMENT_TYPE > & other )

default

template<class ELEMENT_TYPE>

VariantBuilderMultiSampleVector& gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::operator= ( VariantBuilderMultiSampleVector< ELEMENT_TYPE > && other )

default

template<class ELEMENT_TYPE>

void gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::set_sample_value	(	const uint32_t	sample_index,
		const uint32_t	value_index,
		const ELEMENT_TYPE	value
	)

inline

Set a single value for one sample.

Parameters

sample_index	index of the sample (from a VariantHeader lookup)
value_index	index of the value we are setting for this sample (values for EACH sample start at index 0)
value	value to set

Note: MUCH more efficient than set_sample_values() below, since it doesn't require a vector construction/destruction for each call.

Warning: Bounds checking is performed only in debug builds (for the sake of performance), so be sure that sample_index is < num_samples and value_index < max_values_per_sample

template<class ELEMENT_TYPE>

void gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >::set_sample_values	(	const uint32_t	sample_index,
		const std::vector< ELEMENT_TYPE > &	values
	)

inline

Set all values for one sample at once.

Parameters

sample_index	index of the sample (from a VariantHeader lookup)
values	vector of values for this sample

Note: LESS efficient than setting one value at a time using set_sample_value(), since this function involves creating/destroying a vector for each sample.

Warning: Bounds checking is performed only in debug builds (for the sake of performance), so be sure that sample_index is < num_samples and values.size() <= max_values_per_sample

Friends And Related Function Documentation

template<class ELEMENT_TYPE>

friend class VariantBuilder

friend

The documentation for this class was generated from the following file:

gamgee/variant/variant_builder_multi_sample_vector.h

Public Member Functions

Friends

Detailed Description

template<class ELEMENT_TYPE> class gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

template<class ELEMENT_TYPE>
class gamgee::VariantBuilderMultiSampleVector< ELEMENT_TYPE >