D_KmerSet< string_set_type > Struct Template Reference

Detailed description

template< typename string_set_type>
struct D_KmerSet< string_set_type >

Definition at line 38 of file kmers.h.

#include <kmers.h>

Public Methods
	D_KmerSet ()
	D_KmerSet (const string_set_type _string_set, const uint32 _kmer_size)
	D_KmerSet (const string_set_type _string_set, const D_VectorU32 &_active_region_ids)
void	gen_kmer_coords ()
void	gen_kmer_64b_keys ()
void	sort_kmers_by_64b_keys ()
void	segmented_sort_kmers_by_64b_keys ()
template<typename meta_iterator_type >
void	sort_kmers_by_64b_keys_meta (const meta_iterator_type meta_data)
void	sort_kmers_by_64b_keys_seqid ()
template<typename meta_iterator_type >
void	sort_kmers_by_64b_keys_seqid_meta (const meta_iterator_type meta_data)
void	count_kmers_rle ()
void	count_kmers ()
void	count_distinct_by_prefix (D_VectorU32 &prefix_unique_id_map)
void	partition_kmers_by_uniqueness ()
void	gen_prefix_map ()
void	gen_global_unique_map ()
void	gen_global_UID_map ()
void	gen_global_to_sorted_id_map ()
void	mark_unique_kmers ()
void	filter_coords_by_prefix_uniqueness (const D_VectorU8 &unique_map)
void	extract_super_kmers ()
void	collapse_and_extract_non_overlaps (D_VectorSetKmerCoord &kmers_out, D_VectorU32 &prefix_ids_out, D_VectorU32 &suffix_ids_out, D_VectorU32 &counts_out)
void	count_distinct_by_prefix ()
void	init_alloc_temp_space ()
D_VectorU32::iterator	get_scratch_space (uint32 size)
void	reset_scratch_space ()

Public Members
const string_set_type	string_set
D_VectorU32	active_region_ids
uint32	kmer_size
D_VectorSetKmerCoord	coords
D_VectorU64	kmers_64b
D_VectorU64	kmers_64b_distinct
D_VectorU32	kmers_64b_unique_idxs
D_VectorU32	kmers_64b_repeat_idxs
D_VectorU32	global_to_sorted_id_map
D_VectorU32	global_to_UID_map
D_VectorU8	global_unique_flag_map
D_VectorU32	kmers_counts
uint32	n_kmers
uint32	n_distinct
uint32	n_unique
uint32	n_repeat
D_VectorSetKmerCoord	super_coords
D_VectorU32	super_prefix_uids
D_VectorU32	super_suffix_uids
uint32	n_super_coords
D_VectorU32	scratch_u32
uint32	n_alloc
uint32	selector

Constructor & Destructor Documentation

template<typename string_set_type>

D_KmerSet< string_set_type >::D_KmerSet ( )

inline

Definition at line 73 of file kmers.h.

template<typename string_set_type>

D_KmerSet< string_set_type >::D_KmerSet ( const string_set_type  _string_set, const uint32  _kmer_size  )

inline

Definition at line 75 of file kmers.h.

template<typename string_set_type>

D_KmerSet< string_set_type >::D_KmerSet ( const string_set_type  _string_set, const D_VectorU32 &  _active_region_ids  )

inline

Definition at line 79 of file kmers.h.

Member Function Documentation

template<typename string_set_type >

void D_KmerSet< string_set_type >::collapse_and_extract_non_overlaps	(	D_VectorSetKmerCoord &	kmers_out,
		D_VectorU32 &	prefix_ids_out,
		D_VectorU32 &	suffix_ids_out,
		D_VectorU32 &	counts_out
	)

Definition at line 1546 of file kmers_inl.h.

template<typename string_set_type>

void D_KmerSet< string_set_type >::count_distinct_by_prefix

(

D_VectorU32 &

prefix_unique_id_map)

template<typename string_set_type>

void D_KmerSet< string_set_type >::count_distinct_by_prefix

(

)

template<typename string_set_type >

void D_KmerSet< string_set_type >::count_kmers

(

)

Definition at line 1306 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::count_kmers_rle

(

)

Definition at line 1289 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::extract_super_kmers

(

)

Definition at line 1454 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::filter_coords_by_prefix_uniqueness

(

const D_VectorU8 &

unique_map)

Definition at line 1433 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::gen_global_to_sorted_id_map

(

)

Definition at line 1399 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::gen_global_UID_map

(

)

Definition at line 1381 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::gen_global_unique_map

(

)

Definition at line 1364 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::gen_kmer_64b_keys

(

)

Definition at line 1078 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::gen_kmer_coords

(

)

Definition at line 1061 of file kmers_inl.h.

template<typename string_set_type>

void D_KmerSet< string_set_type >::gen_prefix_map

(

)

template<typename string_set_type>

D_VectorU32::iterator D_KmerSet< string_set_type >::get_scratch_space ( uint32  size)

inline

Definition at line 115 of file kmers.h.

template<typename string_set_type>

void D_KmerSet< string_set_type >::init_alloc_temp_space ( )

inline

Definition at line 109 of file kmers.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::mark_unique_kmers

(

)

Definition at line 1409 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::partition_kmers_by_uniqueness

(

)

Definition at line 1324 of file kmers_inl.h.

template<typename string_set_type>

void D_KmerSet< string_set_type >::reset_scratch_space ( )

inline

Definition at line 125 of file kmers.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::segmented_sort_kmers_by_64b_keys

(

)

Definition at line 1117 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::sort_kmers_by_64b_keys

(

)

Definition at line 1091 of file kmers_inl.h.

template<typename string_set_type >

template<typename meta_iterator_type >

void D_KmerSet< string_set_type >::sort_kmers_by_64b_keys_meta

(

const meta_iterator_type

meta_data)

Definition at line 1106 of file kmers_inl.h.

template<typename string_set_type >

void D_KmerSet< string_set_type >::sort_kmers_by_64b_keys_seqid

(

)

Definition at line 1145 of file kmers_inl.h.

template<typename string_set_type >

template<typename meta_iterator_type >

void D_KmerSet< string_set_type >::sort_kmers_by_64b_keys_seqid_meta

(

const meta_iterator_type

meta_data)

Definition at line 1169 of file kmers_inl.h.

Member Data Documentation

template<typename string_set_type>

D_VectorU32 D_KmerSet< string_set_type >::active_region_ids

Definition at line 41 of file kmers.h.

template<typename string_set_type>

D_VectorSetKmerCoord D_KmerSet< string_set_type >::coords

Definition at line 44 of file kmers.h.

template<typename string_set_type>

D_VectorU32 D_KmerSet< string_set_type >::global_to_sorted_id_map

Definition at line 50 of file kmers.h.

template<typename string_set_type>

D_VectorU32 D_KmerSet< string_set_type >::global_to_UID_map

Definition at line 51 of file kmers.h.

template<typename string_set_type>

D_VectorU8 D_KmerSet< string_set_type >::global_unique_flag_map

Definition at line 52 of file kmers.h.

template<typename string_set_type>

uint32 D_KmerSet< string_set_type >::kmer_size

Definition at line 42 of file kmers.h.

template<typename string_set_type>

D_VectorU64 D_KmerSet< string_set_type >::kmers_64b

Definition at line 45 of file kmers.h.

template<typename string_set_type>

D_VectorU64 D_KmerSet< string_set_type >::kmers_64b_distinct

Definition at line 46 of file kmers.h.

template<typename string_set_type>

D_VectorU32 D_KmerSet< string_set_type >::kmers_64b_repeat_idxs

Definition at line 49 of file kmers.h.

template<typename string_set_type>

D_VectorU32 D_KmerSet< string_set_type >::kmers_64b_unique_idxs

Definition at line 48 of file kmers.h.

template<typename string_set_type>

D_VectorU32 D_KmerSet< string_set_type >::kmers_counts

Definition at line 54 of file kmers.h.

template<typename string_set_type>

uint32 D_KmerSet< string_set_type >::n_alloc

Definition at line 70 of file kmers.h.

template<typename string_set_type>

uint32 D_KmerSet< string_set_type >::n_distinct

Definition at line 57 of file kmers.h.

template<typename string_set_type>

uint32 D_KmerSet< string_set_type >::n_kmers

Definition at line 56 of file kmers.h.

template<typename string_set_type>

uint32 D_KmerSet< string_set_type >::n_repeat

Definition at line 59 of file kmers.h.

template<typename string_set_type>

uint32 D_KmerSet< string_set_type >::n_super_coords

Definition at line 66 of file kmers.h.

template<typename string_set_type>

uint32 D_KmerSet< string_set_type >::n_unique

Definition at line 58 of file kmers.h.

template<typename string_set_type>

D_VectorU32 D_KmerSet< string_set_type >::scratch_u32

Definition at line 69 of file kmers.h.

template<typename string_set_type>

uint32 D_KmerSet< string_set_type >::selector

Definition at line 71 of file kmers.h.

template<typename string_set_type>

const string_set_type D_KmerSet< string_set_type >::string_set

Definition at line 40 of file kmers.h.

template<typename string_set_type>

D_VectorSetKmerCoord D_KmerSet< string_set_type >::super_coords

Definition at line 63 of file kmers.h.

template<typename string_set_type>

D_VectorU32 D_KmerSet< string_set_type >::super_prefix_uids

Definition at line 64 of file kmers.h.

template<typename string_set_type>

D_VectorU32 D_KmerSet< string_set_type >::super_suffix_uids

Definition at line 65 of file kmers.h.

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The documentation for this struct was generated from the following files:

• E:/git/nvbio/nvMicroAssembly/kmers.h
• E:/git/nvbio/nvMicroAssembly/kmers_inl.h