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cluster_dbscan_SW.c
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cluster_dbscan_SW.c
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#include<stdio.h>
#include<string.h>
#include<stdlib.h>
#include<ctype.h>
#include<unistd.h>
#include"dataset.h"
#include"cluster.h"
#if defined(_SCAN_SMITH_WATERMAN_GPU)
#ifdef __APPLE__
#include<OpenCL/OpenCL.h>
#else
#include<CL/opencl.h>
#endif
#endif
#include"dbscan.h"
void file_error(char* path) {
printf("failed to open file %s\n",path);
_exit(1);
}
int main(int argc, char** argv) {
dataset ds;
float epsilon;
int minpts;
FILE* fasta_f;
split_set set_of_clusters;
#if defined(_SCAN_SMITH_WATERMAN_GPU)
opencl_stuff ocl;
#endif
if(argc < 4) {
printf("Arguments are: \n"
" [file] Sequences in FASTA \n"
" Epsilon \n"
" minPoints \n"
" output-files prefix \n" );
return(1);
}
sscanf(argv[2], "%f", &epsilon);
sscanf(argv[3], "%i", &minpts);
if ( NULL == (fasta_f = fopen(argv[1], "r"))) file_error(argv[1]);
ds = dataset_from_fasta(fasta_f);
fclose(fasta_f);
#if defined(_SCAN_SMITH_WATERMAN_GPU)
ocl = opencl_initialization(ds);
set_of_clusters = dbscan_SW_GPU(ds, epsilon, minpts, ocl);
opencl_destroy(ocl);
#else
set_of_clusters = dbscan_SW(ds, epsilon, minpts);
#endif
printf("%u clusters obtained \n", set_of_clusters.n_clusters);
if (set_of_clusters.n_clusters < 500) {
create_cluster_files(argv[4], set_of_clusters, ds);
}
free_sequences_from_dataset(ds);
free_split_set_and_associated_clusters(set_of_clusters);
}