/**
* From current edge, get all mates of the used reads.
*/
pool *get_mate_pool_from_edge(edge *eg, const hash_table *ht, const int ori) {
int i = 0;
bwa_seq_t *s = NULL, *mate = NULL, *seqs = NULL;
pool *mate_pool = NULL;
mate_pool = new_pool();
seqs = ht->seqs;
for (i = 0; i < eg->reads->len; i++) {
s = g_ptr_array_index(eg->reads, i);
mate = get_mate(s, seqs);
//p_query("READ", s);
//p_query("MATE", mate);
// If the mate should have been used.
if (is_paired(s, ori))
continue;
// If the insert size is not in the range
if (abs(eg->len - s->shift) > (insert_size + sd_insert_size * SD_TIMES)) {
continue;
}
// If the mate is already in use, either by current or another thread
if (mate->tid != -1 || mate->status == USED || mate->status == DEAD)
continue;
// The read should be used by current edge already
// and the mate has not been used by this template before.
if (!(s->status == TRIED && s->contig_id == eg->id) || (mate->status
== TRIED && mate->contig_id == eg->id))
continue;
mate->rev_com = s->rev_com;
mate_pool_add(mate_pool, mate, eg->tid);
}
return mate_pool;
}
/**
* Keep only those reads with its mates at the right direction and position
*
* ori = 0: For below, 'read' should be right, 'mate' should be left
* ---------------------->
* ----> ---->
* mate read
*/
void keep_mates_in_pool(edge *eg, pool *cur_pool, const hash_table *ht,
const int ori, const int remove_single) {
bwa_seq_t *read = NULL, *mate = NULL;
int i = 0, to_remove = 1;
for (i = 0; i < cur_pool->reads->len; i++) {
read = g_ptr_array_index(cur_pool->reads, i);
mate = get_mate(read, ht->seqs);
// // When extending to left, the initial mate pool and current pool overlap
// if (read->is_in_m_pool == eg->tid)
// continue;
to_remove = 0;
//p_query(__func__, mate);
// The mate of 'read' should be used already
//if (strcmp(read->name, "5896388") == 0) {
// show_debug_msg(__func__, "ORI: %d \n", ori);
// show_debug_msg(__func__, "Edge [%d, %d] \n", eg->id, eg->len);
// p_query(__func__, mate);
// p_query(__func__, read);
//}
if (is_paired(read, ori)) {
// If the mate is not used, remove 'read'
if ((read->rev_com != mate->rev_com) || (mate->status != TRIED)
|| eg->tid != mate->tid) {
//p_query(__func__, read);
//p_query(__func__, mate);
to_remove = 1;
} else { // If the distance is not within range, remove 'read'
if (abs(eg->len - mate->shift) > (insert_size + sd_insert_size
* SD_TIMES)) {
to_remove = 1;
}
}
} else {
to_remove = remove_single;
}
// If the read is obtained by another thread, just remove it
if (to_remove || read->is_in_c_pool != eg->tid) {
read->status = TRIED;
read->contig_id = eg->id;
if (pool_rm_index(cur_pool, i)) {
read->shift = eg->len - read->cursor + 1;
i--;
}
}
}
}
Mapping(const bam_hdr_t * hdr_p, bam1_t * rec_p)
: _rec_p(rec_p)
{
_query_name = bam_get_qname(rec_p);
_flag = rec_p->core.flag;
for (int i = 0; i < rec_p->core.l_qseq; ++i)
{
_seq += seq_nt16_str[bam_seqi(bam_get_seq(rec_p), i)];
}
if (is_mapped())
{
_chr_name = hdr_p->target_name[rec_p->core.tid];
_rf_start = rec_p->core.pos;
_cigar = Cigar(bam_get_cigar(rec_p), rec_p->core.n_cigar);
_rf_len = _cigar.rf_len();
}
if (is_paired() and mp_is_mapped())
{
_mp_chr_name = hdr_p->target_name[rec_p->core.mtid];
_mp_rf_start = rec_p->core.mpos;
}
}
bool treat_as_paired() const
{
return is_paired()
and (not is_mapped() or not mp_is_mapped() or chr_name() == mp_chr_name());
}
