gamgee::utils::MergedVCFAllelesIdxLUT< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered > Class Template Reference

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...

#include <merged_vcf_lut.h>

Inheritance diagram for gamgee::utils::MergedVCFAllelesIdxLUT< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered >:

Public Member Functions
	MergedVCFAllelesIdxLUT (unsigned numInputGVCFs)
void	resize_luts_if_needed (unsigned numMergedAlleles)
Public Member Functions inherited from gamgee::utils::MergedVCFLUTBase< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered >
void	reset_luts ()
	: clear all mappings More...
void	add_input_merged_idx_pair (unsigned inputGVCFIdx, int inputIdx, int mergedIdx)
template<bool M = merged_2_inputs_LUT_is_input_ordered, typename std::enable_if< M >::type * = nullptr>
int	get_input_idx_for_merged (unsigned inputGVCFIdx, int mergedIdx) const
	Get field idx for input VCF inputGVCFIdx corresponding to field idx mergedIdx in the mergedVCF file. More...
template<bool M = merged_2_inputs_LUT_is_input_ordered, typename std::enable_if<!M >::type * = nullptr>
int	get_input_idx_for_merged (unsigned inputGVCFIdx, int mergedIdx) const
template<bool M = inputs_2_merged_LUT_is_input_ordered, typename std::enable_if< M >::type * = nullptr>
int	get_merged_idx_for_input (unsigned inputGVCFIdx, int inputIdx) const
	Get field idx for the merged VCF corresponding to field idx inputIdx in the input VCF of index inputGVCFIdx. More...
template<bool M = inputs_2_merged_LUT_is_input_ordered, typename std::enable_if<!M >::type * = nullptr>
int	get_merged_idx_for_input (unsigned inputGVCFIdx, int inputIdx) const
void	reset_merged_idx_for_input (unsigned inputGVCFIdx, int inputIdx)
	reset/invalidate merged field index for field inputIdx of input VCF inputGVCFIdx More...
void	reset_input_idx_for_merged (unsigned inputGVCFIdx, int mergedIdx)
	reset/invalidate the input field index for input VCF inputGVCFIdx for merged field mergedIdx More...

Additional Inherited Members
Protected Member Functions inherited from gamgee::utils::MergedVCFLUTBase< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered >
	MergedVCFLUTBase ()
	MergedVCFLUTBase (unsigned numInputGVCFs, unsigned numMergedFields)
	~MergedVCFLUTBase ()=default
void	clear ()
	deallocates memory More...
template<bool M = inputs_2_merged_LUT_is_input_ordered, typename std::enable_if< M >::type * = nullptr>
void	resize_inputs_2_merged_lut_if_needed (unsigned numInputGVCFs, unsigned numMergedFields)
	resize LUT functions More...
template<bool M = inputs_2_merged_LUT_is_input_ordered, typename std::enable_if<!M >::type * = nullptr>
void	resize_inputs_2_merged_lut_if_needed (unsigned numInputGVCFs, unsigned numMergedFields)
template<bool M = merged_2_inputs_LUT_is_input_ordered, typename std::enable_if< M >::type * = nullptr>
void	resize_merged_2_inputs_lut_if_needed (unsigned numInputGVCFs, unsigned numMergedFields)
template<bool M = merged_2_inputs_LUT_is_input_ordered, typename std::enable_if<!M >::type * = nullptr>
void	resize_merged_2_inputs_lut_if_needed (unsigned numInputGVCFs, unsigned numMergedFields)
void	resize_luts_if_needed (unsigned numInputGVCFs, unsigned numMergedFields)
Protected Attributes inherited from gamgee::utils::MergedVCFLUTBase< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered >
unsigned	m_num_input_vcfs
unsigned	m_num_merged_fields

Detailed Description

template<bool inputs_2_merged_LUT_is_input_ordered, bool merged_2_inputs_LUT_is_input_ordered>
class gamgee::utils::MergedVCFAllelesIdxLUT< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered >

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.

Constructor & Destructor Documentation

template<bool inputs_2_merged_LUT_is_input_ordered, bool merged_2_inputs_LUT_is_input_ordered>

gamgee::utils::MergedVCFAllelesIdxLUT< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered >::MergedVCFAllelesIdxLUT ( unsigned  numInputGVCFs )

inline

Member Function Documentation

template<bool inputs_2_merged_LUT_is_input_ordered, bool merged_2_inputs_LUT_is_input_ordered>

void gamgee::utils::MergedVCFAllelesIdxLUT< inputs_2_merged_LUT_is_input_ordered, merged_2_inputs_LUT_is_input_ordered >::resize_luts_if_needed ( unsigned  numMergedAlleles )

inline

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

• gamgee/utils/merged_vcf_lut.h