pair<Edit, Edit> cut_edit_at_from(const Edit& e, size_t from_off) {
Edit left, right;
if (from_off > e.from_length()) {
return make_pair(e, right);
}
// from-length of left portion
size_t l = e.from_length() - from_off;
// from-length of right portion
size_t r = e.from_length() - l;
if (edit_is_match(e)) {
left.set_from_length(l);
left.set_to_length(l);
right.set_from_length(r);
right.set_to_length(r);
} else if (edit_is_sub(e)) {
left.set_from_length(l);
left.set_to_length(l);
left.set_sequence(e.sequence().substr(0, l));
right.set_from_length(r);
right.set_to_length(r);
right.set_sequence(e.sequence().substr(l));
} else if (edit_is_insertion(e)) {
left = e;
} else if (edit_is_deletion(e)) {
left.set_from_length(l);
right.set_from_length(r);
}
return make_pair(left, right);
}
vector<Edit> Sampler::mutate_edit(const Edit& edit,
const pos_t& position,
double base_error,
double indel_error,
const string& bases,
uniform_real_distribution<double>& rprob,
uniform_int_distribution<int>& rbase) {
// we will build up a mapping representing the modified edit
Mapping new_mapping;
//*new_mapping.mutable_position() = make_position(position);
// determine to-length of edit
size_t to_length = edit.to_length();
// we will keep track of the current base using this
pos_t curr_pos = position;
/// TODO we should punt if we aren't a pure edit
// as in, we are something with mixed to and from lengths; like a block sub with an indel
if (edit_is_match(edit) || edit_is_sub(edit)
|| edit_is_insertion(edit)) {
// distribute mutations across this length
for (size_t k = 0; k < to_length; ++k) {
char c = 'N'; // in the case that we are in an insertion
if (!edit_is_insertion(edit)) {
c = pos_char(curr_pos);
++get_offset(curr_pos);
}
if (rprob(rng) <= base_error) {
// pick another base than what c is
char n;
do {
n = bases[rbase(rng)];
} while (n == c);
// make the edit for the sub
Edit* e = new_mapping.add_edit();
string s(1, n);
e->set_sequence(s);
e->set_from_length(1);
e->set_to_length(1);
// if we've got a indel
// note that we're using a simple geometric indel dsitribution here
} else if (rprob(rng) <= indel_error) {
if (rprob(rng) < 0.5) {
char n = bases[rbase(rng)];
Edit* e = new_mapping.add_edit();
string s(1, c);
e->set_sequence(s);
e->set_to_length(1);
} else {
Edit* e = new_mapping.add_edit();
e->set_from_length(1);
}
} else {
// make the edit for the 1bp match
Edit* e = new_mapping.add_edit();
e->set_from_length(1);
e->set_to_length(1);
}
}
} else if (edit_is_deletion(edit)) {
// special case: 0 (deletion)
// maybe we do nothing; as there is no length in the read
}
// simplify the mapping
new_mapping = simplify(new_mapping);
// copy the new edits
vector<Edit> new_edits;
for (size_t i = 0; i < new_mapping.edit_size(); ++i) {
new_edits.push_back(new_mapping.edit(i));
}
// and send them back
return new_edits;
}
