void
tmap_refseq_pac2revpac(const char *fn_fasta)
{
uint32_t i, j, c;
tmap_refseq_t *refseq=NULL, *refseq_rev=NULL;
tmap_progress_print("reversing the packed reference FASTA");
refseq = tmap_refseq_read(fn_fasta, 0);
// shallow copy
refseq_rev = tmap_calloc(1, sizeof(tmap_refseq_t), "refseq_rev");
(*refseq_rev) = (*refseq);
// update sequence
refseq_rev->seq = NULL;
refseq_rev->seq = tmap_calloc(tmap_refseq_seq_memory(refseq->len), sizeof(uint8_t), "refseq_rev->seq");
for(i=0;i<refseq->len;i++) {
c = tmap_refseq_seq_i(refseq, i);
j = refseq->len - i - 1;
tmap_refseq_seq_store_i(refseq_rev, j, c);
}
// write
tmap_refseq_write(refseq_rev, fn_fasta, 1);
// free
free(refseq_rev->seq);
free(refseq_rev);
tmap_refseq_destroy(refseq);
tmap_progress_print2("reversed the packed reference FASTA");
}
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;
}
int
tmap_refseq_pac2fasta_main(int argc, char *argv[])
{
int c, help=0, amb=0;
uint32_t i, j, k;
char *fn_fasta = NULL;
tmap_refseq_t *refseq = NULL;
while((c = getopt(argc, argv, "avh")) >= 0) {
switch(c) {
case 'a': amb = 1; break;
case 'v': tmap_progress_set_verbosity(1); break;
case 'h': help = 1; break;
default: return 1;
}
}
if(1 != argc - optind || 1 == help) {
tmap_file_fprintf(tmap_file_stderr, "Usage: %s %s [-avh] <in.fasta>\n", PACKAGE, argv[0]);
return 1;
}
fn_fasta = argv[optind];
// Note: 'tmap_file_stdout' should not have been previously modified
tmap_file_stdout = tmap_file_fdopen(fileno(stdout), "wb", TMAP_FILE_NO_COMPRESSION);
// read in the reference sequence
refseq = tmap_refseq_read(fn_fasta, 0);
for(i=0;i<refseq->num_annos;i++) {
tmap_file_fprintf(tmap_file_stdout, ">%s", refseq->annos[i].name->s); // new line handled later
for(j=k=0;j<refseq->annos[i].len;j++) {
if(0 == (j % TMAP_REFSEQ_FASTA_LINE_LENGTH)) {
tmap_file_fprintf(tmap_file_stdout, "\n");
}
if(1 == amb && 0 < refseq->annos[i].num_amb) {
// move the next ambiguous region
while(k < refseq->annos[i].num_amb && refseq->annos[i].amb_positions_end[k] < j+1) {
k++;
}
// check for the ambiguous region
if(k < refseq->annos[i].num_amb
&& 0 == tmap_interval_overlap(j+1, j+1, refseq->annos[i].amb_positions_start[k], refseq->annos[i].amb_positions_end[k])) {
tmap_file_fprintf(tmap_file_stdout, "%c", tmap_iupac_int_to_char[refseq->annos[i].amb_bases[k]]);
}
else {
tmap_file_fprintf(tmap_file_stdout, "%c", "ACGTN"[(int)tmap_refseq_seq_i(refseq, j + refseq->annos[i].offset)]);
}
}
else {
tmap_file_fprintf(tmap_file_stdout, "%c", "ACGTN"[(int)tmap_refseq_seq_i(refseq, j + refseq->annos[i].offset)]);
}
}
tmap_file_fprintf(tmap_file_stdout, "\n");
}
// destroy
tmap_refseq_destroy(refseq);
// close the output
tmap_file_fclose(tmap_file_stdout);
return 0;
}
