kmers_inl.h File Reference

#include <cstdlib>
#include <nvbio/basic/thrust_view.h>
#include <nvbio/basic/primitives.h>
#include <nvbio/basic/atomics.h>
#include <nvbio/basic/cuda/sort.h>
#include <nvbio/basic/cuda/primitives.h>
#include <nvbio/strings/seeds.h>
#include "assembly_types.h"

Go to the source code of this file.

Classes
struct	get_kmer_seq_id
struct	get_kmer_reg_id
struct	get_kmer_size
struct	get_global_id
struct	set_global_id
struct	set_global_id_region_id
struct	get_prefix_global_id
struct	get_prefix_global_id_by_idx
struct	get_suffix_global_id_by_idx
struct	compute_prefix_global_id
struct	compute_suffix_global_id
struct	global_to_uid
struct	global_to_sorted_id
struct	kmers_to_64b_functor< string_set_type >
struct	kmer_key_sid_eq
struct	kmer_key_rid_eq
struct	kmer_pos_sid_eq
struct	kmer_uid_eq
struct	kmer_word_extractor_functor< string_set_type >
struct	kmer_count_tuple_sum
struct	is_unique_kmer
struct	mark_kmer_uniqueness
struct	store_kmer_unique_ids
struct	populate_unique_kmer_data
struct	mark_unique_prefix_kmer
struct	extract_super_kmers_functor< string_set_type >
struct	print_super_kmer_functor< string_set_type >
struct	is_invalid_super_kmer
struct	is_unique_suffix_id
struct	is_unique_uid
struct	is_repeat_kmer
struct	collapse_same_start_kmers
struct	find_max_kmer_overlaps< string_set_type >
struct	num_non_overlapped_repeats
struct	num_adj_repeats
struct	extract_non_overlapped_repeats< string_set_type >
struct	count_overlapped_adjacencies
struct	extract_repeat_adjacencies
struct	extract_unique_adjacencies
struct	super_coord_to_seq< string_set_type >
struct	test_funct

Functions
template<typename string_set_type >
D_VectorU32::iterator	sort_kmers_lexicographic (const string_set_type string_set, D_VectorSetKmerCoord &coords, const uint32 n_kmers, const uint32 fixed_kmer_size, D_VectorU32 &indices)
template<typename string_set_type >
void	segmented_sort_super_kmers_lexicographic (const string_set_type string_set, uint32 n_coords, D_VectorSetKmerCoord &super_coords, D_VectorU32 &super_prefix_ids, D_VectorU32 &super_suffix_ids)

Function Documentation

template<typename string_set_type >

void segmented_sort_super_kmers_lexicographic	(	const string_set_type	string_set,
		uint32	n_coords,
		D_VectorSetKmerCoord &	super_coords,
		D_VectorU32 &	super_prefix_ids,
		D_VectorU32 &	super_suffix_ids
	)

Definition at line 1251 of file kmers_inl.h.

template<typename string_set_type >

D_VectorU32::iterator sort_kmers_lexicographic	(	const string_set_type	string_set,
		D_VectorSetKmerCoord &	coords,
		const uint32	n_kmers,
		const uint32	fixed_kmer_size,
		D_VectorU32 &	indices
	)

Definition at line 1191 of file kmers_inl.h.