co_elf_symbol_t *co_get_symbol_by_name(co_elf_data_t *pl, const char *name)
{
int index =0 ;
uintptr_t symbols;
symbols = pl->symbol_table_section->sh_size / sizeof(Elf32_Sym);
for (index=0; index < symbols; index++) {
Elf32_Sym *symbol = co_get_symbol(pl, index);
if (strcmp(name, co_get_string(pl, symbol->st_name)) == 0)
return (co_elf_symbol_t *)symbol;
}
return NULL;
}
int main(int argc, char* argv[])
{
time_t start;
struct llist **headptr;
int *sortedocc, *sortedfreq, ngoodlmers;
long *sortedindex;
FILE* fp;
start = time(0);
/* Gather command-line options... */
if( 0 == 1*
co_get_string(argc, argv, "-sequence", &SEQUENCE_FILE) *
co_get_string(argc, argv, "-freq", &LMER_TABLE_FILE)
) {
usage();
}
co_get_int(argc, argv, "-tandem", &TANDEMDIST) || (TANDEMDIST = 500);
co_get_int(argc, argv, "-min", &MINTHRESH) || (MINTHRESH = 3);
co_get_bool(argc, argv, "-sort", &SORT);
co_get_bool(argc, argv, "-v", &VERBOSE);
co_get_int(argc, argv, "-start", &START);
co_get_int(argc, argv, "-stop", &STOP);
fp = fopen( SEQUENCE_FILE, "ro" );
if( NULL == fp ) {
fprintf(stderr, "Could not open sequence file %s\n", SEQUENCE_FILE);
exit(1);
}
fseek(fp, 0, SEEK_END);
MAXLENGTH = ftell(fp); /* This is an approximation, but an overestimate, so we're ok! */
fclose(fp);
co_get_int(argc, argv, "-l", &l) || (l = default_l(MAXLENGTH));
sequence = (char *)malloc( (MAXLENGTH + PADLENGTH) * sizeof(char) );
if( NULL == sequence ) {
fprintf(stderr, "Unable to allocate %d bytes for the sequence\n", MAXLENGTH + PADLENGTH );
exit(1);
}
/* build sequence */
length = build_sequence(sequence,SEQUENCE_FILE);
/* build headptr */
if((headptr = (struct llist **) malloc(HASH_SIZE*sizeof(*headptr))) == NULL)
{
fprintf(stderr,"Out of memory\n"); exit(1);
}
if(VERBOSE) fprintf(stderr," Done allocating headptr\n");
build_headptr(headptr); if(VERBOSE) fprintf(stderr," Done building headptr\n");
/* sort headptr */
ngoodlmers = count_headptr(headptr);
if(VERBOSE) fprintf(stderr," There are %d l-mers\n",ngoodlmers);
if((sortedfreq = (int *) malloc(ngoodlmers*sizeof(*sortedfreq))) == NULL)
{
fprintf(stderr,"Out of memory\n"); exit(1);
}
if((sortedocc = (int *) malloc(ngoodlmers*sizeof(*sortedocc))) == NULL)
{
fprintf(stderr,"Out of memory\n"); exit(1);
}
if((sortedindex = (long *) malloc(ngoodlmers*sizeof(*sortedindex))) == NULL)
{
fprintf(stderr,"Out of memory\n"); exit(1);
}
sort_headptr(headptr, sortedfreq, sortedocc, sortedindex, ngoodlmers);
if(VERBOSE) fprintf(stderr," Done sorting headptr\n");
if(ngoodlmers == 0) { fprintf(stderr,"OOPS no good lmers\n"); exit(1); }
print_lmers(headptr, sortedfreq, sortedocc, sortedindex, ngoodlmers);
exit(0);
}