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edit.cpp
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#include "vg/io/edit.hpp"
namespace vg {
namespace io {
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;
}
bool edit_is_empty(const Edit& e) {
return e.to_length() == 0 && e.from_length() == 0 && e.sequence().empty();
}
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);
}
// breaking dependence on vg's utility.hpp
static const char complement[256] = {'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 8
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 16
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 24
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 32
'N', 'N', 'N', '$', '#', 'N', 'N', 'N', // 40 GCSA stop/start characters
'N', 'N', 'N', 'N', 'N', '-', 'N', 'N', // 48
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 56
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 64
'N', 'T', 'V', 'G', 'H', 'N', 'N', 'C', // 72
'D', 'N', 'N', 'M', 'N', 'K', 'N', 'N', // 80
'N', 'Q', 'Y', 'W', 'A', 'A', 'B', 'S', // 88
'N', 'R', 'N', 'N', 'N', 'N', 'N', 'N', // 96
'N', 't', 'v', 'g', 'h', 'N', 'N', 'c', // 104
'd', 'N', 'N', 'm', 'N', 'k', 'n', 'N', // 112
'N', 'q', 'y', 'w', 'a', 'a', 'b', 's', // 120
'N', 'r', 'N', 'N', 'N', 'N', 'N', 'N', // 128
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 136
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 144
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 152
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 160
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 168
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 176
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 184
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 192
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 200
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 208
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 216
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 224
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 232
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 240
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 248
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N'};// 256
static inline char reverse_complement(const char& c) {
return complement[c];
}
static string reverse_complement(const string& seq) {
string rc;
rc.assign(seq.rbegin(), seq.rend());
for (auto& c : rc) {
c = complement[c];
}
return rc;
}
Edit reverse_complement_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;
}
bool operator==(const Edit& e1, const Edit& e2) {
return (e1.to_length() == e2.to_length())
&& (e1.from_length() == e2.from_length())
&& (e1.sequence() == e2.sequence());
}
}
}