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edit.cpp
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edit.cpp
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#include "edit.hpp"
#include "utility.hpp"
namespace vg {
bool edit_is_match(const Edit& e) {
return e.from_length() == e.to_length() && e.sequence().empty();
}
bool edit_is_sub(const Edit& e) {
return e.from_length() == e.to_length() && !e.sequence().empty();
}
bool edit_is_insertion(const Edit& e) {
return e.from_length() == 0 && e.to_length() > 0 && !e.sequence().empty();
}
bool edit_is_deletion(const Edit& e) {
return e.from_length() > 0 && e.to_length() == 0;
}
pair<Edit, Edit> cut_edit_at_to(const Edit& e, size_t to_off) {
Edit left, right;
if (to_off > e.to_length()) {
return make_pair(e, right);
}
// to-length of left portion
size_t l = e.to_length() - to_off;
// to-length of right portion
size_t r = e.to_length() - l;
if (l > e.to_length()) {
left = e;
} else 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.set_to_length(l);
left.set_sequence(e.sequence().substr(0, l));
right.set_to_length(r);
right.set_sequence(e.sequence().substr(l));
} else if (edit_is_deletion(e)) {
left = e;
}
return make_pair(left, right);
}
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);
}
Edit reverse_edit(const Edit& e) {
// Make a reversed copy
Edit reversed = e;
// All we have to do is flip the sequence
reversed.set_sequence(reverse_complement(e.sequence()));
return reversed;
}
}