BWA::BWA(const char* ann_filename,
const char* amb_filename,
const char* pac_filename,
const char* forward_bwt_filename,
const char* forward_sa_filename,
const char* reverse_bwt_filename,
const char* reverse_sa_filename)
{
// Load the bns (?) and reference
bns = bns_restore_core(ann_filename,amb_filename,pac_filename);
reference = new ubyte_t[bns->l_pac/4+1];
rewind(bns->fp_pac);
fread(reference, 1, bns->l_pac/4+1, bns->fp_pac);
fclose(bns->fp_pac);
bns->fp_pac = NULL;
// Load the BWTs (both directions) and suffix arrays (both directions)
bwts[0] = bwt_restore_bwt(forward_bwt_filename);
bwt_restore_sa(forward_sa_filename, bwts[0]);
bwts[1] = bwt_restore_bwt(reverse_bwt_filename);
bwt_restore_sa(reverse_sa_filename, bwts[1]);
load_default_options();
// Always reinitialize the random seed whenever a new set of files are loaded.
initialize_random_seed();
// initialize the bwase subsystem
bwase_initialize();
}
bntseq_t *bns_restore(const char *prefix)
{
char ann_filename[1024], amb_filename[1024], pac_filename[1024], alt_filename[1024];
FILE *fp;
bntseq_t *bns;
strcat(strcpy(ann_filename, prefix), ".ann");
strcat(strcpy(amb_filename, prefix), ".amb");
strcat(strcpy(pac_filename, prefix), ".pac");
bns = bns_restore_core(ann_filename, amb_filename, pac_filename);
if (bns == 0) return 0;
if ((fp = fopen(strcat(strcpy(alt_filename, prefix), ".alt"), "r")) != 0) { // read .alt file if present
char str[1024];
khash_t(str) *h;
int i, absent;
khint_t k;
h = kh_init(str);
for (i = 0; i < bns->n_seqs; ++i) {
k = kh_put(str, h, bns->anns[i].name, &absent);
kh_val(h, k) = i;
}
while (fscanf(fp, "%s", str) == 1) {
k = kh_get(str, h, str);
if (k != kh_end(h))
bns->anns[kh_val(h, k)].is_alt = 1;
}
kh_destroy(str, h);
fclose(fp);
}
return bns;
}
bntseq_t *bns_restore(const char *prefix)
{
char ann_filename[1024], amb_filename[1024], pac_filename[1024];
strcat(strcpy(ann_filename, prefix), ".ann");
strcat(strcpy(amb_filename, prefix), ".amb");
strcat(strcpy(pac_filename, prefix), ".pac");
return bns_restore_core(ann_filename, amb_filename, pac_filename);
}
bntseq_t *bns_restore(const char *prefix)
{
char ann_filename[1024], amb_filename[1024], pac_filename[1024], alt_filename[1024];
FILE *fp;
bntseq_t *bns;
/**** bisulfite adaptation ****/
/* strcat(strcpy(ann_filename, prefix), ".ann"); */
/* strcat(strcpy(amb_filename, prefix), ".amb"); */
/* strcat(strcpy(pac_filename, prefix), ".pac"); */
strcat(strcpy(ann_filename, prefix), ".bis.ann");
strcat(strcpy(amb_filename, prefix), ".bis.amb");
strcat(strcpy(pac_filename, prefix), ".bis.pac");
bns = bns_restore_core(ann_filename, amb_filename, pac_filename);
if (bns == 0) return 0;
if ((fp = fopen(strcat(strcpy(alt_filename, prefix), ".alt"), "r")) != 0) { // read .alt file if present
char str[1024];
khash_t(str) *h;
int c, i, absent;
khint_t k;
h = kh_init(str);
for (i = 0; i < bns->n_seqs; ++i) {
k = kh_put(str, h, bns->anns[i].name, &absent);
kh_val(h, k) = i;
}
i = 0;
while ((c = fgetc(fp)) != EOF) {
if (c == '\t' || c == '\n' || c == '\r') {
str[i] = 0;
if (str[0] != '@') {
k = kh_get(str, h, str);
if (k != kh_end(h))
bns->anns[kh_val(h, k)].is_alt = 1;
}
while (c != '\n' && c != EOF) c = fgetc(fp);
i = 0;
} else str[i++] = c; // FIXME: potential segfault here
}
kh_destroy(str, h);
fclose(fp);
}
return bns;
}
