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;
}
int
tmap_map_vsw_main(int argc, char *argv[])
{
tmap_map_driver_t *driver = NULL;
// init
driver = tmap_map_driver_init(TMAP_MAP_ALGO_MAPVSW, tmap_map_vsw_mapq);
driver->opt->algo_stage = 1;
// get options
if(1 != tmap_map_opt_parse(argc, argv, driver->opt) // options parsed successfully
|| argc != optind // all options should be used
|| 1 == argc) { // some options should be specified
return tmap_map_opt_usage(driver->opt);
}
else {
// check command line arguments
tmap_map_opt_check(driver->opt);
}
// run map_vsw
tmap_map_vsw_core(driver);
// destroy
tmap_map_driver_destroy(driver);
tmap_progress_print2("terminating successfully");
return 0;
}
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");
}
int
tmap_vswbm_main(int argc, char *argv[])
{
int32_t seq_len = 150;
int32_t tlen = 256;
int32_t n_iter = 1000;
int32_t n_sub_iter = 1;
int32_t vsw_type = 0;
int c;
while((c = getopt(argc, argv, "q:t:n:N:H:h")) >= 0) {
switch(c) {
case 'q':
seq_len = atoi(optarg); break;
case 't':
tlen = atoi(optarg); break;
case 'n':
n_iter = atoi(optarg); break;
case 'N':
n_sub_iter = atoi(optarg); break;
case 'H':
vsw_type = atoi(optarg); break;
case 'h':
default:
return usage(seq_len, tlen, n_iter, n_sub_iter, vsw_type);
}
}
if(argc != optind || seq_len > tlen) {
return usage(seq_len, tlen, n_iter, n_sub_iter, vsw_type);
}
tmap_progress_set_verbosity(1);
tmap_progress_print2("starting benchmark");
tmap_vsw_bm_core(seq_len, tlen, n_iter, n_sub_iter, vsw_type);
tmap_progress_print2("ending benchmark");
return 0;
}
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");
}
int
tmap_index(int argc, char *argv[])
{
int c;
tmap_index_opt_t opt;
opt.fn_fasta = NULL;
opt.occ_interval = TMAP_BWT_OCC_INTERVAL;
opt.hash_width = INT32_MAX;
opt.sa_interval = TMAP_SA_INTERVAL;
opt.is_large = -1;
opt.check_hash = 1;
if(2 == argc && 0 == strcmp("--version", argv[1])) {
tmap_file_stdout = tmap_file_fdopen(fileno(stdout), "wb", TMAP_FILE_NO_COMPRESSION);
tmap_file_fprintf(tmap_file_stdout, "%s\n", tmap_refseq_get_version_format(PACKAGE_VERSION));
tmap_file_fclose(tmap_file_stdout);
return 0;
}
while((c = getopt(argc, argv, "f:o:i:w:a:hvH")) >= 0) {
switch(c) {
case 'f':
opt.fn_fasta = tmap_strdup(optarg); break;
case 'o':
opt.occ_interval = atoi(optarg); break;
case 'i':
opt.sa_interval = atoi(optarg); break;
case 'w':
opt.hash_width = atoi(optarg); break;
case 'a':
if(0 == strcmp("is", optarg)) opt.is_large = 0;
else if(0 == strcmp("bwtsw", optarg)) opt.is_large = 1;
else tmap_error("Option -a value not correct", Exit, CommandLineArgument);
break;
case 'v':
tmap_progress_set_verbosity(1); break;
case 'h':
return usage(&opt);
case 'H':
opt.check_hash = 0; break;
default:
return usage(&opt);
}
}
if(argc != optind || 1 == argc) {
return usage(&opt);
}
if(NULL == opt.fn_fasta) {
tmap_error("required option -f", Exit, CommandLineArgument);
}
if(opt.occ_interval < TMAP_BWT_OCC_MOD || 0 != (opt.occ_interval % 2) || 0 != (opt.occ_interval % TMAP_BWT_OCC_MOD)) {
tmap_error("option -o out of range", Exit, CommandLineArgument);
}
if(opt.hash_width < 0) {
tmap_error("option -w out of range", Exit, CommandLineArgument);
}
if(opt.sa_interval <= 0 || (1 < opt.sa_interval && 0 != (opt.sa_interval % 2))) {
tmap_error("option -i out of range", Exit, CommandLineArgument);
}
tmap_index_core(&opt);
free(opt.fn_fasta);
tmap_progress_print2("terminating successfully");
return 0;
}
void
tmap_bwt_compare_core2(tmap_bwt_t *bwt[2], int32_t length, int32_t print_msg, int32_t warn)
{
uint8_t *seqs[2] = {NULL,NULL};
char *str = NULL;
int32_t i, asymmetric, k, m;
uint64_t hash_j;
int64_t sum, j;
tmap_bwt_match_occ_t sa[2];
tmap_bwt_int_t n[2][2];
for(i=1;i<=length;i++) {
seqs[0] = tmap_calloc(i, sizeof(uint8_t), "seqs[0]");
seqs[1] = tmap_calloc(i, sizeof(uint8_t), "seqs[1]");
str = tmap_calloc(i+1, sizeof(char), "str");
for(j=0;j<i;j++) {
seqs[1][j] = 3;
}
asymmetric = 0;
j = 0;
hash_j = sum = 0;
while(1) {
if(i == j) {
for(k=0;k<i;k++) {
seqs[1][k] = 3 - seqs[0][i-k-1];
}
for(k=0;k<2;k++) {
for(m=0;m<2;m++) {
n[m][k] = tmap_bwt_match_exact_reverse(bwt[m], i, seqs[k], &sa[m]);
}
if(n[0][k] != n[1][k] || sa[0].k != sa[1].k || sa[0].l != sa[1].l || sa[0].hi != sa[1].hi || sa[0].offset != sa[1].offset) {
tmap_progress_print2("BWTs did not match");
tmap_progress_print2("n=[%llu,%llu]", n[0][k], n[1][k]);
tmap_progress_print2("k=[%llu,%llu]", sa[0].k, sa[1].k);
tmap_progress_print2("l=[%llu,%llu]", sa[0].l, sa[1].l);
tmap_progress_print2("hi=[%llu,%llu]", sa[0].hi, sa[1].hi);
tmap_progress_print2("offset=[%llu,%llu]", sa[0].offset, sa[1].offset);
tmap_bug();
}
}
for(k=0;k<2;k++) {
// use m == 0 && k = 0
if(0 == k) {
if(0 < n[0][k] && TMAP_BWT_INT_MAX != sa[0].k && sa[0].k <= sa[0].l) {
sum += n[0][k];
}
}
}
if(0 == asymmetric && n[0][0] != n[0][1]) {
asymmetric = 1;
//fprintf(stderr, "n[0][0]=%u n[0][1]=%u\n", n[0][0], n[0][1]);
tmap_error("Asymmetry found", Warn, OutOfRange);
}
j--;
while(0 <= j && 3 == seqs[0][j]) {
seqs[0][j] = 0;
hash_j >>= 2;
j--;
}
if(j < 0) break;
seqs[0][j]++;
hash_j++;
j++;
}
else {
hash_j <<= 2;
j++;
}
}
free(seqs[0]);
free(seqs[1]);
free(str);
j = (sum == (bwt[0]->seq_len - i + 1)) ? 0 : 1; // j==1 on fail
if(1 == print_msg) {
if(0 == j) tmap_progress_print2("%d-mer validation passed", i);
else tmap_progress_print2("%d-mer validation failed: observed (%llu) != expected (%llu)\n", i, sum, bwt[0]->seq_len - i + 1);
}
if(0 == warn && 1 == j) {
tmap_error("inconsistency found in the BWT", Exit, OutOfRange);
}
}
void
tmap_bwt_check_core2(tmap_bwt_t *bwt, int32_t length, int32_t print_msg, int32_t print_sa, int32_t warn)
{
uint8_t *seqs[2] = {NULL,NULL};
char *str = NULL;
int32_t i, asymmetric, k, l;
uint64_t hash_j;
int64_t sum, j;
tmap_bwt_match_occ_t sa;
tmap_bwt_int_t n[2];
for(i=1;i<=length;i++) {
seqs[0] = tmap_calloc(i, sizeof(uint8_t), "seqs[0]");
seqs[1] = tmap_calloc(i, sizeof(uint8_t), "seqs[1]");
str = tmap_calloc(i+1, sizeof(char), "str");
for(j=0;j<i;j++) {
seqs[1][j] = 3;
}
asymmetric = 0;
j = 0;
hash_j = sum = 0;
while(1) {
if(i == j) {
for(k=0;k<i;k++) {
seqs[1][k] = 3 - seqs[0][i-k-1];
}
for(k=0;k<2;k++) {
//n[k] = tmap_bwt_match_exact(bwt, i, seqs[k], &sa);
n[k] = tmap_bwt_match_exact_reverse(bwt, i, seqs[k], &sa);
if(0 == k) {
if(0 < n[k] && TMAP_BWT_INT_MAX != sa.k && sa.k <= sa.l) {
sum += n[k];
}
if(1 == print_msg && 1 == print_sa) {
for(l=0;l<i;l++) {
str[l] = "ACGTN"[seqs[k][l]];
}
if(0 < n[k] && TMAP_BWT_INT_MAX != sa.k && sa.k <= sa.l) {
tmap_progress_print2("%s\t%llu\t%llu\t%llu", str, sa.k, sa.l, n[k]);
#ifdef TMAP_BWT_CHECK_DEBUG
while(sa.k <= sa.l) {
uint32_t seqid, pos;
uint8_t strand;
tmap_bwt_int_t pacpos = tmap_sa_pac_pos(tmap_bwt_index->sa, bwt, sa.k);
if(0 < tmap_refseq_pac2real(tmap_bwt_index->refseq, pacpos, 1, &seqid, &pos, &strand)) {
tmap_progress_print2("%s\t%llu\t%llu\t%llu\t%c%u:%u", str, sa.k, sa.l, n[k],
"+-"[strand], seqid, pos);
}
else {
tmap_progress_print2("%s\t%llu\t%llu\t%llu\t%c%u:%u", str, sa.k, sa.l, n[k],
'?', 0, 0);
}
sa.k++;
}
#endif
}
else {
tmap_progress_print2("%s\tNA\tNA\tNA", str);
}
}
}
}
if(0 == asymmetric && n[0] != n[1]) {
asymmetric = 1;
//fprintf(stderr, "n[0]=%u n[1]=%u\n", n[0], n[1]);
tmap_error("Asymmetry found", Warn, OutOfRange);
}
j--;
while(0 <= j && 3 == seqs[0][j]) {
seqs[0][j] = 0;
hash_j >>= 2;
j--;
}
if(j < 0) break;
seqs[0][j]++;
hash_j++;
j++;
}
else {
hash_j <<= 2;
j++;
}
}
free(seqs[0]);
free(seqs[1]);
free(str);
j = (sum == (bwt->seq_len - i + 1)) ? 0 : 1; // j==1 on fail
if(1 == print_msg) {
if(0 == j) tmap_progress_print2("%d-mer validation passed", i);
else tmap_progress_print2("%d-mer validation failed: observed (%llu) != expected (%llu)\n", i, sum, bwt->seq_len - i + 1);
}
if(0 == warn && 1 == j) {
tmap_error("inconsistency found in the BWT", Exit, OutOfRange);
}
}
uint64_t
tmap_refseq_fasta2pac(const char *fn_fasta, int32_t compression)
{
tmap_file_t *fp_pac = NULL, *fp_anno = NULL;
tmap_seq_io_t *seqio = NULL;
tmap_seq_t *seq = NULL;
tmap_refseq_t *refseq = NULL;
char *fn_pac = NULL, *fn_anno = NULL;
uint8_t buffer[TMAP_REFSEQ_BUFFER_SIZE];
int32_t i, j, l, buffer_length;
uint32_t num_IUPAC_found= 0, amb_bases_mem = 0;
uint8_t x = 0;
uint64_t ref_len;
tmap_progress_print("packing the reference FASTA");
refseq = tmap_calloc(1, sizeof(tmap_refseq_t), "refseq");
refseq->version_id = TMAP_VERSION_ID;
refseq->package_version = tmap_string_clone2(PACKAGE_VERSION);
refseq->seq = buffer; // IMPORTANT: must nullify later
refseq->annos = NULL;
refseq->num_annos = 0;
refseq->len = 0;
refseq->is_rev = 0;
refseq->is_shm = 0;
memset(buffer, 0, TMAP_REFSEQ_BUFFER_SIZE);
buffer_length = 0;
// input files
seqio = tmap_seq_io_init(fn_fasta, TMAP_SEQ_TYPE_FQ, 0, compression);
seq = tmap_seq_init(TMAP_SEQ_TYPE_FQ);
// output files
fn_pac = tmap_get_file_name(fn_fasta, TMAP_PAC_FILE);
fp_pac = tmap_file_fopen(fn_pac, "wb", TMAP_PAC_COMPRESSION);
// read in sequences
while(0 <= (l = tmap_seq_io_read(seqio, seq))) {
tmap_anno_t *anno = NULL;
tmap_progress_print2("packing contig [%s:1-%d]", seq->data.fq->name->s, l);
refseq->num_annos++;
refseq->annos = tmap_realloc(refseq->annos, sizeof(tmap_anno_t)*refseq->num_annos, "refseq->annos");
anno = &refseq->annos[refseq->num_annos-1];
anno->name = tmap_string_clone(seq->data.fq->name);
anno->len = l;
anno->offset = (1 == refseq->num_annos) ? 0 : refseq->annos[refseq->num_annos-2].offset + refseq->annos[refseq->num_annos-2].len;
anno->amb_positions_start = NULL;
anno->amb_positions_end = NULL;
anno->amb_bases = NULL;
anno->num_amb = 0;
amb_bases_mem = 0;
// fill the buffer
for(i=0;i<l;i++) {
uint8_t c = tmap_nt_char_to_int[(int)seq->data.fq->seq->s[i]];
// handle IUPAC codes
if(4 <= c) {
int32_t k;
// warn users about IUPAC codes
if(0 == num_IUPAC_found) {
tmap_error("IUPAC codes were found and will be converted to non-matching DNA bases", Warn, OutOfRange);
for(j=4;j<15;j++) {
c = tmap_iupac_char_to_bit_string[(int)tmap_iupac_int_to_char[j]];
// get the lexicographically smallest base not compatible with this code
for(k=0;k<4;k++) {
if(!(c & (0x1 << k))) {
break;
}
}
tmap_progress_print2("IUPAC code %c will be converted to %c", tmap_iupac_int_to_char[j], "ACGTN"[k & 3]);
}
}
num_IUPAC_found++;
// change it to a mismatched base than the IUPAC code
c = tmap_iupac_char_to_bit_string[(int)seq->data.fq->seq->s[i]];
// store IUPAC bases
if(amb_bases_mem <= anno->num_amb) { // allocate more memory if necessary
amb_bases_mem = anno->num_amb + 1;
tmap_roundup32(amb_bases_mem);
anno->amb_positions_start = tmap_realloc(anno->amb_positions_start, sizeof(uint32_t) * amb_bases_mem, "anno->amb_positions_start");
anno->amb_positions_end = tmap_realloc(anno->amb_positions_end, sizeof(uint32_t) * amb_bases_mem, "anno->amb_positions_end");
anno->amb_bases = tmap_realloc(anno->amb_bases, sizeof(uint8_t) * amb_bases_mem, "anno->amb_bases");
}
// encode stretches of the same base
if(0 < anno->num_amb
&& anno->amb_positions_end[anno->num_amb-1] == i
&& anno->amb_bases[anno->num_amb-1] == tmap_iupac_char_to_int[(int)seq->data.fq->seq->s[i]]) {
anno->amb_positions_end[anno->num_amb-1]++; // expand the range
}
else {
// new ambiguous base and range
anno->num_amb++;
anno->amb_positions_start[anno->num_amb-1] = i+1; // one-based
anno->amb_positions_end[anno->num_amb-1] = i+1; // one-based
anno->amb_bases[anno->num_amb-1] = tmap_iupac_char_to_int[(int)seq->data.fq->seq->s[i]];
}
// get the lexicographically smallest base not compatible with
// this code
for(j=0;j<4;j++) {
if(!(c & (0x1 << j))) {
break;
}
}
c = j & 3; // Note: Ns will go to As
}
if(3 < c) {
tmap_error("bug encountered", Exit, OutOfRange);
}
if(buffer_length == (TMAP_REFSEQ_BUFFER_SIZE << 2)) { // 2-bit
if(tmap_refseq_seq_memory(buffer_length) != tmap_file_fwrite(buffer, sizeof(uint8_t), tmap_refseq_seq_memory(buffer_length), fp_pac)) {
tmap_error(fn_pac, Exit, WriteFileError);
}
memset(buffer, 0, TMAP_REFSEQ_BUFFER_SIZE);
buffer_length = 0;
}
tmap_refseq_seq_store_i(refseq, buffer_length, c);
buffer_length++;
}
refseq->len += l;
// re-size the amibiguous bases
if(anno->num_amb < amb_bases_mem) {
amb_bases_mem = anno->num_amb;
anno->amb_positions_start = tmap_realloc(anno->amb_positions_start, sizeof(uint32_t) * amb_bases_mem, "anno->amb_positions_start");
anno->amb_positions_end = tmap_realloc(anno->amb_positions_end, sizeof(uint32_t) * amb_bases_mem, "anno->amb_positions_end");
anno->amb_bases = tmap_realloc(anno->amb_bases, sizeof(uint8_t) * amb_bases_mem, "anno->amb_bases");
}
}
// write out the buffer
if(tmap_refseq_seq_memory(buffer_length) != tmap_file_fwrite(buffer, sizeof(uint8_t), tmap_refseq_seq_memory(buffer_length), fp_pac)) {
tmap_error(fn_pac, Exit, WriteFileError);
}
if(refseq->len % 4 == 0) { // add an extra byte if we completely filled all bits
if(1 != tmap_file_fwrite(&x, sizeof(uint8_t), 1, fp_pac)) {
tmap_error(fn_pac, Exit, WriteFileError);
}
}
// store number of unused bits at the last byte
x = refseq->len % 4;
if(1 != tmap_file_fwrite(&x, sizeof(uint8_t), 1, fp_pac)) {
tmap_error(fn_pac, Exit, WriteFileError);
}
refseq->seq = NULL; // IMPORTANT: nullify this
ref_len = refseq->len; // save for return
tmap_progress_print2("total genome length [%u]", refseq->len);
if(0 < num_IUPAC_found) {
if(1 == num_IUPAC_found) {
tmap_progress_print("%u IUPAC base was found and converted to a DNA base", num_IUPAC_found);
}
else {
tmap_progress_print("%u IUPAC bases were found and converted to DNA bases", num_IUPAC_found);
}
}
// write annotation file
fn_anno = tmap_get_file_name(fn_fasta, TMAP_ANNO_FILE);
fp_anno = tmap_file_fopen(fn_anno, "wb", TMAP_ANNO_COMPRESSION);
tmap_refseq_write_anno(fp_anno, refseq);
// close files
tmap_file_fclose(fp_pac);
tmap_file_fclose(fp_anno);
// check sequence name uniqueness
for(i=0;i<refseq->num_annos;i++) {
for(j=i+1;j<refseq->num_annos;j++) {
if(0 == strcmp(refseq->annos[i].name->s, refseq->annos[j].name->s)) {
tmap_file_fprintf(tmap_file_stderr, "Contigs have the same name: #%d [%s] and #%d [%s]\n",
i+1, refseq->annos[i].name->s,
j+1, refseq->annos[j].name->s);
tmap_error("Contig names must be unique", Exit, OutOfRange);
}
}
}
tmap_refseq_destroy(refseq);
tmap_seq_io_destroy(seqio);
tmap_seq_destroy(seq);
free(fn_pac);
free(fn_anno);
tmap_progress_print2("packed the reference FASTA");
tmap_refseq_pac2revpac(fn_fasta);
return ref_len;
}
