static tmap_map1_aux_stack_t*
tmap_map1_aux_stack_reset(tmap_map1_aux_stack_t *stack,
int32_t max_mm, int32_t max_gapo, int32_t max_gape,
const tmap_map_opt_t *opt)
{
int32_t i;
//int32_t i, j;
int32_t n_bins_needed = 0;
// move to the beginning of the memory pool
stack->entry_pool_i = 0;
stack->best_score = INT32_MAX;
if(TMAP_MAP1_AUX_STACK_TOO_BIG < stack->entry_pool_length) {
tmap_map1_aux_stack_destroy_helper(stack, 0);
tmap_map1_aux_stack_init_helper(stack);
}
// clear the bins
for(i=0;i<stack->n_bins;i++) {
/*
for(j=0;j<stack->bins[i].n_entries;j++) {
stack->bins[i].entries[j] = NULL;
}
*/
stack->bins[i].n_entries = 0;
}
// resize the bins if necessary
n_bins_needed = aln_score(max_mm+1, max_gapo+1, max_gape+1, opt);
if(stack->n_bins < n_bins_needed) {
// realloc
tmap_roundup32(n_bins_needed);
stack->bins = tmap_realloc(stack->bins, sizeof(tmap_map1_aux_bin_t) * n_bins_needed, "stack->bins");
// initialize
for(i=stack->n_bins;i<n_bins_needed;i++) {
stack->bins[i].n_entries = stack->bins[i].m_entries = 0;
stack->bins[i].entries = NULL;
}
stack->n_bins = n_bins_needed;
}
stack->n_entries = 0;
return stack;
}
void
tmap_map2_aln_realloc(tmap_map2_aln_t *a, int32_t n)
{
int32_t i;
if(NULL == a) return;
if(n < a->n) {
for(i=n;i<a->n;i++) {
tmap_map2_hit_nullify(&a->hits[i]);
}
a->n = n;
}
else if(a->max < n) { // allocate more memory
i = a->max; // save for init
a->max = (0 == a->max && n < 4) ? 4 : tmap_roundup32(n);
// resize
a->hits = tmap_realloc(a->hits, sizeof(tmap_map2_hit_t) * a->max, "a->hits");
// init
while(i < a->max) {
tmap_map2_hit_nullify(&a->hits[i]);
i++;
}
}
}
static inline void
tmap_map1_aux_stack_push(tmap_map1_aux_stack_t *stack,
int32_t offset,
tmap_bwt_match_occ_t *match_sa_prev,
int32_t n_mm, int32_t n_gapo, int32_t n_gape,
int32_t state, int32_t is_diff,
tmap_map1_aux_stack_entry_t *prev_entry,
const tmap_map_opt_t *opt)
{
int32_t i;
int32_t n_bins_needed = 0;
tmap_map1_aux_stack_entry_t *entry = NULL;
tmap_map1_aux_bin_t *bin = NULL;
// check to see if we need more memory
if(stack->entry_pool_length <= stack->entry_pool_i) {
int32_t i = stack->entry_pool_length;
stack->entry_pool_length <<= 2;
stack->entry_pool = tmap_realloc(stack->entry_pool,
sizeof(tmap_map1_aux_stack_entry_t*)*stack->entry_pool_length,
"stack->entry_pool");
while(i<stack->entry_pool_length) {
stack->entry_pool[i] = tmap_malloc(sizeof(tmap_map1_aux_stack_entry_t), "stack->entry_pool[i]");
i++;
}
}
entry = stack->entry_pool[stack->entry_pool_i];
entry->score = aln_score(n_mm, n_gapo, n_gape, opt);
entry->n_mm = n_mm;
entry->n_gapo = n_gapo;
entry->n_gape = n_gape;
entry->state = state;
entry->match_sa = (*match_sa_prev);
entry->i = stack->entry_pool_i;
entry->offset = offset;
if(NULL == prev_entry) {
entry->last_diff_offset = offset;
entry->prev_i = -1;
}
else {
entry->last_diff_offset = (1 == is_diff) ? (offset) : prev_entry->last_diff_offset;
entry->prev_i = prev_entry->i;
}
if(stack->n_bins <= entry->score) {
//tmap_bug();
// resize the bins if necessary
n_bins_needed = entry->score + 1;
// realloc
tmap_roundup32(n_bins_needed);
stack->bins = tmap_realloc(stack->bins, sizeof(tmap_map1_aux_bin_t) * n_bins_needed, "stack->bins");
// initialize
for(i=stack->n_bins;i<n_bins_needed;i++) {
stack->bins[i].n_entries = stack->bins[i].m_entries = 0;
stack->bins[i].entries = NULL;
}
stack->n_bins = n_bins_needed;
}
if(stack->n_bins <= entry->score) {
tmap_bug();
}
bin = &stack->bins[entry->score];
// - remove duplicates
// - most likely formed by tandem repeats or indels
// - too computationally expensive, and not necessary
/*
for(i=0;i<bin->n_entries;i++) {
if(bin->entries[i]->match_sa.k == entry->match_sa.k
&& bin->entries[i]->match_sa.l == entry->match_sa.l
&& bin->entries[i]->offset == entry->offset
&& bin->entries[i]->state == entry->state) {
return;
}
}
*/
// update best score
if(stack->best_score > entry->score) stack->best_score = entry->score;
if(bin->m_entries <= bin->n_entries) {
bin->m_entries++;
tmap_roundup32(bin->m_entries);
bin->entries = tmap_realloc(bin->entries, sizeof(tmap_map1_aux_bin_t) * bin->m_entries, "bin->entries");
}
bin->entries[bin->n_entries] = entry;
bin->n_entries++;
stack->entry_pool_i++;
stack->n_entries++;
}
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;
}
void
tmap_sam_update_cigar_and_md(bam1_t *b, char *ref, char *read, int32_t len)
{
int32_t i, n_cigar, last_type;
uint32_t *cigar;
int32_t diff;
int32_t soft_clip_start_i, soft_clip_end_i;
if(b->data_len - b->l_aux != bam1_aux(b) - b->data) {
tmap_error("b->data_len - b->l_aux != bam1_aux(b) - b->data", Exit, OutOfRange);
}
// keep track of soft clipping
n_cigar = soft_clip_start_i = soft_clip_end_i = 0;
cigar = bam1_cigar(b);
if(BAM_CSOFT_CLIP == TMAP_SW_CIGAR_OP(cigar[0])) {
soft_clip_start_i = 1;
n_cigar++;
}
if(1 < b->core.n_cigar && BAM_CSOFT_CLIP == TMAP_SW_CIGAR_OP(cigar[b->core.n_cigar-1])) {
soft_clip_end_i = 1;
n_cigar++;
}
cigar = NULL;
// get the # of cigar operators
last_type = tmap_sam_get_type(ref[0], read[0]);
n_cigar++;
for(i=1;i<len;i++) {
int32_t cur_type = tmap_sam_get_type(ref[i], read[i]);
if(cur_type != last_type) {
n_cigar++;
}
last_type = cur_type;
}
// resize the data field if necessary
if(n_cigar < b->core.n_cigar) {
diff = sizeof(uint32_t) * (b->core.n_cigar - n_cigar);
// shift down
for(i=b->core.l_qname;i<b->data_len - diff;i++) {
b->data[i] = b->data[i + diff];
}
b->data_len -= diff;
b->core.n_cigar = n_cigar;
}
else if(b->core.n_cigar < n_cigar) {
diff = sizeof(uint32_t) * (n_cigar - b->core.n_cigar);
// realloc
if(b->m_data <= (b->data_len + diff)) {
b->m_data = b->data_len + diff + 1;
tmap_roundup32(b->m_data);
b->data = tmap_realloc(b->data, sizeof(uint8_t) * b->m_data, "b->data");
}
// shift up
for(i=b->data_len-1;b->core.l_qname<=i;i--) {
b->data[i + diff] = b->data[i];
}
b->data_len += diff;
b->core.n_cigar = n_cigar;
}
if(b->data_len - b->l_aux != bam1_aux(b) - b->data) {
tmap_error("b->data_len - b->l_aux != bam1_aux(b) - b->data", Exit, OutOfRange);
}
// create the cigar
cigar = bam1_cigar(b);
for(i=soft_clip_start_i;i<n_cigar-soft_clip_end_i;i++) {
cigar[i] = 0;
}
n_cigar = soft_clip_start_i; // skip over soft clipping etc.
last_type = tmap_sam_get_type(ref[0], read[0]);
TMAP_SW_CIGAR_STORE(cigar[n_cigar], last_type, 1);
for(i=1;i<len;i++) {
int32_t cur_type = tmap_sam_get_type(ref[i], read[i]);
if(cur_type == last_type) {
// add to the cigar length
TMAP_SW_CIGAR_ADD_LENGTH(cigar[n_cigar], 1);
}
else {
// add to the cigar
n_cigar++;
TMAP_SW_CIGAR_STORE(cigar[n_cigar], cur_type, 1);
}
last_type = cur_type;
}
// Note: the md tag must be updated
tmap_sam_md1(b, ref, len);
}