int main(int argc, char **argv) { setvbuf(stdout, NULL, _IOLBF, 0); CmdLine* cmd_line = cmd_line_alloc(); if (cmd_line==NULL) { return -1; } parse_cmdline(cmd_line, argc, argv, sizeof(Element)); dBGraph * db_graph = NULL; //Create the de Bruijn graph/hash table int max_retries=15; db_graph = hash_table_new(cmd_line->mem_height, cmd_line->mem_width, max_retries, cmd_line->kmer_size); if (db_graph==NULL) { return -1; } //some setup int file_reader_fasta(FILE * fp, Sequence * seq, int max_read_length, boolean new_entry, boolean * full_entry){ long long ret; int offset = 0; if (new_entry == false){ offset = db_graph->kmer_size; //die("new_entry must be true in hsi test function"); } ret = read_sequence_from_fasta(fp, seq, max_read_length,new_entry,full_entry,offset); return ret; }
int main(int argc, char **argv) { setvbuf(stdout, NULL, _IOLBF, 0); CmdLine* cmd_line = cmd_line_alloc(); if (cmd_line==NULL) { return -1; } // VERSION_STR is passed from the makefile -- usually last commit hash parse_cmdline(cmd_line, argc,argv,sizeof(Element)); if (cmd_line->format==Stdout){ printf("myKrobe.predictor for Staphylococcus, version %d.%d.%d.%d"VERSION_STR"\n", VERSION, SUBVERSION, SUBSUBVERSION, SUBSUBSUBVERSION); } dBGraph * db_graph = NULL; boolean (*subsample_function)(); //local func boolean subsample_as_specified() { double ran = drand48(); if (ran <= cmd_line->subsample_propn) { return true; } return false; } //end of local func if (cmd_line->subsample==true) { subsample_function = &subsample_as_specified; } else { subsample_function = &subsample_null; } // int lim = cmd_line->max_expected_sup_len; /* CovgArray* working_ca_for_median=alloc_and_init_covg_array(lim);//will die if fails to alloc if (working_ca_for_median==NULL) { return -1; }*/ //Create the de Bruijn graph/hash table int max_retries=15; db_graph = hash_table_new(cmd_line->mem_height, cmd_line->mem_width, max_retries, cmd_line->kmer_size); if (db_graph==NULL) { return -1; } //some setup int file_reader_fasta(FILE * fp, Sequence * seq, int max_read_length, boolean new_entry, boolean * full_entry){ long long ret; int offset = 0; if (new_entry == false){ offset = db_graph->kmer_size; //die("new_entry must be true in hsi test function"); } ret = read_sequence_from_fasta(fp,seq,max_read_length,new_entry,full_entry,offset); return ret; }