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#include <stdlib.h>
#include "common.cu"
extern "C" {
struct QuerySet
{
int qfile;
char * h_tex_array;
char* d_tex_array;
int* d_addrs_tex_array;
int* h_addrs_tex_array;
int* h_lengths_array;
int* d_lengths_array;
char** h_names;
unsigned int count;
size_t texlen;
// total device memory occupied by this query set
size_t bytes_on_board;
};
struct AuxiliaryNodeData
{
int length;
int depth;
int leafid;
char leafchar;
TextureAddress parent;
};
struct Reference
{
/* Reference string */
char* str;
size_t len;
unsigned int pitch;
void* d_ref_tex_array; //cudaArray*
char* h_ref_tex_array;
/* Suffix tree for reference */
void* d_node_tex_array; //really a cudaArray*
void* h_node_tex_array; //really a PixelOfNode*
void* d_children_tex_array; //cudaArray*
void* h_children_tex_array; //PixelOfChildren*
unsigned int tex_height;
unsigned int tex_width;
// total device memory occupied by this query set
size_t bytes_on_board;
AuxiliaryNodeData* aux_data;
int num_nodes;
};
// Matches are reported as a node in the suffix tree,
// plus a distance up the node's parent link for partial
// matches on the patch from the root to the node
struct MatchCoord
{
unsigned int node; // match node
short edge_match_length; // number of missing characters UP the parent edge
};
struct MatchResults
{
// Each MatchCoord in the buffers below corresponds to the first character
// of some substring of one of the queries
MatchCoord* d_match_coords;
MatchCoord* h_match_coords;
size_t numCoords;
// total device memory occupied by this query set
size_t bytes_on_board;
};
typedef unsigned int MUMMERGPU_OPTIONS;
enum MUMMerGPUOption {
DEFAULT,
ON_CPU = (1<<0)
};
//All times in milliseconds
struct Statistics
{
float t_kernel;
float t_output;
float t_to_board;
float t_from_board;
float t_moving_tree_pages;
float t_query_read;
float t_total;
float t_construction;
float bp_avg_query_length;
};
struct MatchContext
{
char* full_ref;
size_t full_ref_len;
Reference* ref;
QuerySet* queries;
MatchResults results;
bool on_cpu;
int min_match_length;
bool reverse;
bool forwardreverse;
bool forwardcoordinates;
bool show_query_length;
bool maxmatch;
char* stats_file;
Statistics statistics;
};
struct ReferencePage
{
int begin;
int end;
int shadow_left;
int shadow_right;
MatchResults results;
unsigned int id;
Reference ref;
};
int createReference(const char* fromFile, Reference* ref);
int destroyReference(Reference* ref);
int createQuerySet(const char* fromFile, QuerySet* queries);
int destroyQuerySet(QuerySet* queries);
int createMatchContext(Reference* ref,
QuerySet* queries,
MatchResults* matches,
MUMMERGPU_OPTIONS options,
int min_match_length,
char* stats_file,
bool reverse,
bool forwardreverse,
bool forwardcoordinates,
bool showQueryLength,
MatchContext* ctx);
int destroyMatchContext(MatchContext* ctx);
int matchQueries(MatchContext* ctx);
void printStringForError(int err);
}
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