tmap_index_t*
tmap_index_init(const char *fn_fasta, key_t shm_key, int32_t mm)
{
tmap_index_t *index = NULL;
index = tmap_calloc(1, sizeof(tmap_index_t), "index");
index->shm_key = shm_key;
index->mm = mm;
// get the reference information
// primary 65380; sa_intv: 32
// seq_len = 97004
//n_sa = 3032, sa 67973 .. 18446744073709551615
if (1 == index->mm) {
tmap_progress_print("Retrieving reference data from memory map");
index->refseq = tmap_refseq_mm_read(fn_fasta);
index->bwt = tmap_bwt_mm_read(fn_fasta);
index->sa = tmap_sa_mm_read(fn_fasta);
tmap_progress_print2("Reference data retrieved from memory map");
} else if(0 == index->shm_key) {
tmap_progress_print("reading in reference data");
index->refseq = tmap_refseq_read(fn_fasta);
index->bwt = tmap_bwt_read(fn_fasta);
index->sa = tmap_sa_read(fn_fasta);
tmap_progress_print2("reference data read in");
}
else {
tmap_progress_print("retrieving reference data from shared memory");
index->shm = tmap_shm_init(index->shm_key, 0, 0);
if(NULL == (index->refseq = tmap_refseq_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_REFSEQ)))) {
tmap_error("the packed reference sequence was not found in shared memory", Exit, SharedMemoryListing);
}
if(NULL == (index->bwt = tmap_bwt_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_BWT)))) {
tmap_error("the BWT string was not found in shared memory", Exit, SharedMemoryListing);
}
if(NULL == (index->sa = tmap_sa_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_SA)))) {
tmap_error("the SA was not found in shared memory", Exit, SharedMemoryListing);
}
tmap_progress_print2("reference data retrieved from shared memory");
}
if((index->refseq->len << 1) != index->bwt->seq_len) {
tmap_error("refseq and bwt lengths do not match", Exit, OutOfRange);
}
if((index->refseq->len << 1) != index->sa->seq_len) {
tmap_error("refseq and sa lengths do not match", Exit, OutOfRange);
}
return index;
}
tmap_index_t*
tmap_index_init(const char *fn_fasta, key_t shm_key)
{
tmap_index_t *index = NULL;
index = tmap_calloc(1, sizeof(tmap_index_t), "index");
index->shm_key = shm_key;
// get the reference information
if(0 == index->shm_key) {
tmap_progress_print("reading in reference data");
index->refseq = tmap_refseq_read(fn_fasta);
index->bwt = tmap_bwt_read(fn_fasta);
index->sa = tmap_sa_read(fn_fasta);
tmap_progress_print2("reference data read in");
}
else {
tmap_progress_print("retrieving reference data from shared memory");
index->shm = tmap_shm_init(index->shm_key, 0, 0);
if(NULL == (index->refseq = tmap_refseq_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_REFSEQ)))) {
tmap_error("the packed reference sequence was not found in shared memory", Exit, SharedMemoryListing);
}
if(NULL == (index->bwt = tmap_bwt_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_BWT)))) {
tmap_error("the BWT string was not found in shared memory", Exit, SharedMemoryListing);
}
if(NULL == (index->sa = tmap_sa_shm_unpack(tmap_shm_get_buffer(index->shm, TMAP_SHM_LISTING_SA)))) {
tmap_error("the SA was not found in shared memory", Exit, SharedMemoryListing);
}
tmap_progress_print2("reference data retrieved from shared memory");
}
if((index->refseq->len << 1) != index->bwt->seq_len) {
tmap_error("refseq and bwt lengths do not match", Exit, OutOfRange);
}
if((index->refseq->len << 1) != index->sa->seq_len) {
tmap_error("refseq and sa lengths do not match", Exit, OutOfRange);
}
return index;
}
void
tmap_sa_bwt2sa(const char *fn_fasta, uint32_t intv)
{
int64_t isa, s; // S(isa) = sa
uint64_t i;
tmap_bwt_t *bwt = NULL;
tmap_sa_t *sa = NULL;
tmap_progress_print("constructing the SA from the BWT string");
bwt = tmap_bwt_read(fn_fasta);
sa = tmap_calloc(1, sizeof(tmap_sa_t), "sa");
sa->primary = bwt->primary;
sa->sa_intv = intv;
sa->seq_len = bwt->seq_len;
sa->n_sa = (bwt->seq_len + intv) / intv;
// calculate SA value
sa->sa = tmap_calloc(sa->n_sa, sizeof(tmap_bwt_int_t), "sa->sa");
isa = 0;
s = bwt->seq_len;
for(i = 0; i < bwt->seq_len; ++i) {
if(isa % intv == 0) sa->sa[isa/intv] = s;
--s;
isa = tmap_bwt_invPsi(bwt, isa);
}
if(isa % intv == 0) sa->sa[isa/intv] = s;
sa->sa[0] = (tmap_bwt_int_t)-1; // before this line, bwt->sa[0] = bwt->seq_len
tmap_sa_write(fn_fasta, sa);
tmap_bwt_destroy(bwt);
tmap_sa_destroy(sa);
sa=NULL;
bwt=NULL;
tmap_progress_print2("constructed the SA from the BWT string");
}
