std::size_t
get_ref_seq_known_size(const reference_contig_segment& ref,
const pos_range pr)
{
pos_t b(0);
pos_t end(ref.end());
if (pr.is_begin_pos && (pr.begin_pos>0)) b=pr.begin_pos;
if (pr.is_end_pos && (pr.end_pos>0)) end=std::min(end,pr.end_pos);
std::size_t size(0);
for (; b<end; ++b)
{
if (ref.get_base(b) != 'N') size++;
}
return size;
}
static
void
set_repeat_info(const indel_key& ik,
const reference_contig_segment& ref,
starling_indel_report_info& iri)
{
iri.is_repeat_unit = false;
iri.repeat_unit = "N/A";
iri.ref_repeat_count = 0;
iri.indel_repeat_count = 0;
if(! ((iri.it == INDEL::INSERT) ||
(iri.it == INDEL::DELETE) ||
(iri.it == INDEL::SWAP))) return;
unsigned insert_repeat_count(0);
unsigned delete_repeat_count(0);
if (iri.it == INDEL::INSERT) {
get_seq_repeat_unit(iri.indel_seq,iri.repeat_unit,insert_repeat_count);
} else if(iri.it == INDEL::DELETE) {
get_seq_repeat_unit(iri.ref_seq,iri.repeat_unit,delete_repeat_count);
} else if(iri.it == INDEL::SWAP) {
std::string insert_ru;
std::string delete_ru;
get_seq_repeat_unit(iri.indel_seq,insert_ru,insert_repeat_count);
get_seq_repeat_unit(iri.ref_seq,delete_ru,delete_repeat_count);
if((insert_ru != delete_ru) || insert_ru.empty()) return;
iri.repeat_unit=insert_ru;
} else {
assert(0);
}
// count repeats in contextual sequence:
unsigned indel_context_repeat_count(0);
{
const pos_t indel_begin_pos(ik.pos);
const pos_t indel_end_pos(ik.right_pos());
const int repeat_unit_size(static_cast<int>(iri.repeat_unit.size()));
// count upstream repeats:
for(pos_t i(indel_begin_pos-repeat_unit_size); i>=0; i-=repeat_unit_size) {
bool is_repeat(true);
for(int j(0); j<repeat_unit_size; ++j) {
if(ref.get_base(i+j) != iri.repeat_unit[j]) {
is_repeat = false;
break;
}
}
if(! is_repeat) break;
indel_context_repeat_count += 1;
}
// count downstream repeats:
const pos_t rs(ref.end());
for(pos_t i(indel_end_pos); (i+static_cast<pos_t>(repeat_unit_size)-1)<rs; i+=repeat_unit_size) {
bool is_repeat(true);
for(int j(0); j<repeat_unit_size; ++j) {
if(ref.get_base(i+j) != iri.repeat_unit[j]) {
is_repeat = false;
break;
}
}
if(! is_repeat) break;
indel_context_repeat_count += 1;
}
}
iri.is_repeat_unit = true;
iri.ref_repeat_count = indel_context_repeat_count+delete_repeat_count;
iri.indel_repeat_count = indel_context_repeat_count+insert_repeat_count;
}
