tmap_sa_t *
tmap_sa_shm_unpack(uint8_t *buf)
{
tmap_sa_t *sa = NULL;
if(NULL == buf) return NULL;
sa = tmap_calloc(1, sizeof(tmap_sa_t), "sa");
// fixed length data
memcpy(&sa->primary, buf, sizeof(tmap_bwt_int_t));
buf += sizeof(tmap_bwt_int_t);
memcpy(&sa->sa_intv, buf, sizeof(tmap_bwt_int_t));
buf += sizeof(tmap_bwt_int_t);
memcpy(&sa->seq_len, buf, sizeof(tmap_bwt_int_t));
buf += sizeof(tmap_bwt_int_t);
memcpy(&sa->n_sa, buf, sizeof(tmap_bwt_int_t));
buf += sizeof(tmap_bwt_int_t);
// variable length data
sa->sa = (tmap_bwt_int_t*)buf;
buf += sa->n_sa*sizeof(tmap_bwt_int_t);
sa->sa_intv_log2 = tmap_log2(sa->sa_intv);
sa->is_shm = 1;
sa->is_mm = 0;
return sa;
}
tmap_sa_t *
tmap_sa_read(const char *fn_fasta)
{
char *fn_sa = NULL;
tmap_file_t *fp_sa = NULL;
tmap_sa_t *sa = NULL;
fn_sa = tmap_get_file_name(fn_fasta, TMAP_SA_FILE);
fp_sa = tmap_file_fopen(fn_sa, "rb", TMAP_SA_COMPRESSION);
sa = tmap_calloc(1, sizeof(tmap_sa_t), "sa");
if(1 != tmap_file_fread(&sa->primary, sizeof(tmap_bwt_int_t), 1, fp_sa)
|| 1 != tmap_file_fread(&sa->sa_intv, sizeof(tmap_bwt_int_t), 1, fp_sa)
|| 1 != tmap_file_fread(&sa->seq_len, sizeof(tmap_bwt_int_t), 1, fp_sa)) {
tmap_error(NULL, Exit, ReadFileError);
}
sa->n_sa = (sa->seq_len + sa->sa_intv) / sa->sa_intv;
sa->sa = tmap_calloc(sa->n_sa, sizeof(tmap_bwt_int_t), "sa->sa");
sa->sa[0] = -1;
if(sa->n_sa-1 != tmap_file_fread(sa->sa + 1, sizeof(tmap_bwt_int_t), sa->n_sa - 1, fp_sa)) {
tmap_error(NULL, Exit, ReadFileError);
}
sa->sa_intv_log2 = tmap_log2(sa->sa_intv);
tmap_file_fclose(fp_sa);
free(fn_sa);
sa->is_shm = 0;
return sa;
}
inline size_t
tmap_shm_get_listing_bytes(tmap_shm_t *shm, uint32_t listing)
{
int32_t i;
size_t s = 0;
if(0 == tmap_shm_listing_exists(shm, listing)) return SIZE_MAX;
for(i=1;i<listing;i<<=1) {
if(1 == tmap_shm_listing_exists(shm, i)) {
s += ((size_t*)(((volatile uint32_t*)shm->ptr) + 2))[tmap_log2(i)];
}
}
return s;
}
tmap_sa_t *
tmap_sa_mm_read(const char *fn_fasta)
{
char *buf;
char *fn_sa = NULL;
// allocate some memory
tmap_sa_t *sa = NULL;
sa = tmap_calloc(1, sizeof(tmap_bwt_t), "sa");
sa->is_shm = 0;
sa->is_mm = 1;
// read annotation file
fn_sa = tmap_get_file_name(fn_fasta, TMAP_SA_FILE);
int fd = open(fn_sa, O_RDONLY);
if (fd == -1)
tmap_error("Cannot open file", Exit, ReadFileError);
struct stat sbuf;
if (fstat(fd, &sbuf) == -1) {
tmap_error("Cannot read file stats", Exit, ReadFileError);
}
buf = (char*) mmap(0, sbuf.st_size, PROT_READ, MAP_SHARED, fd, 0);
if (buf == MAP_FAILED)
tmap_error("Cannot map file to memory", Exit, ReadFileError);
/*
if(1 != tmap_file_fread(&sa->primary, sizeof(tmap_bwt_int_t), 1, fp_sa)
|| 1 != tmap_file_fread(&sa->sa_intv, sizeof(tmap_bwt_int_t), 1, fp_sa)
|| 1 != tmap_file_fread(&sa->seq_len, sizeof(tmap_bwt_int_t), 1, fp_sa)) {
tmap_error(NULL, Exit, ReadFileError);
}
sa->n_sa = (sa->seq_len + sa->sa_intv) / sa->sa_intv;
sa->sa = tmap_calloc(sa->n_sa, sizeof(tmap_bwt_int_t), "sa->sa");
sa->sa[0] = -1;
if(sa->n_sa-1 != tmap_file_fread(sa->sa + 1, sizeof(tmap_bwt_int_t), sa->n_sa - 1, fp_sa)) {
tmap_error(NULL, Exit, ReadFileError);
}
sa->sa_intv_log2 = tmap_log2(sa->sa_intv);
*/
// fixed length data
memcpy(&sa->primary, buf, sizeof(tmap_bwt_int_t));
buf += sizeof(tmap_bwt_int_t);
memcpy(&sa->sa_intv, buf, sizeof(tmap_bwt_int_t));
buf += sizeof(tmap_bwt_int_t);
memcpy(&sa->seq_len, buf, sizeof(tmap_bwt_int_t));
buf += sizeof(tmap_bwt_int_t);
sa->n_sa = (sa->seq_len + sa->sa_intv) / sa->sa_intv;
sa->sa = tmap_calloc(sa->n_sa, sizeof(tmap_bwt_int_t), "sa->sa");
sa->sa[0] = -1;
memcpy(sa->sa+1, buf, sizeof(tmap_bwt_int_t)*sa->n_sa -1 );
sa->sa_intv_log2 = tmap_log2(sa->sa_intv);
free(fn_sa);
return sa;
}
inline void
tmap_shm_add_listing(tmap_shm_t *shm, uint32_t listing, size_t size)
{
((volatile uint32_t*)shm->ptr)[1] |= listing;
((size_t*)(((volatile uint32_t*)shm->ptr) + 2))[tmap_log2(listing)] = size;
}