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Make identity() calculation ignore soft clips #4502

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merged 2 commits into from
Jan 23, 2025
Merged

Make identity() calculation ignore soft clips #4502

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eb1b06d
Make `identity()` calculation ignore soft clips
faithokamoto Jan 22, 2025
9f93836
Note change in function
faithokamoto Jan 22, 2025
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7 changes: 6 additions & 1 deletion src/path.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2290,7 +2290,6 @@ double divergence(const Mapping& m) {
}

double identity(const Path& path) {
double ident = 0;
size_t total_length = path_to_length(path);
size_t matched_length = 0;
for (size_t i = 0; i < path.mapping_size(); ++i) {
Expand All @@ -2299,6 +2298,12 @@ double identity(const Path& path) {
auto& edit = mapping.edit(j);
if (edit_is_match(edit)) {
matched_length += edit.from_length();
} else if (edit_is_insertion(edit)) {
bool is_first_edit = (i == 0) && (j == 0);
bool is_last_edit = (i == path.mapping_size() - 1) && (j == mapping.edit_size() - 1);
if (is_first_edit || is_last_edit) {
total_length -= edit.to_length();
}
}
}
}
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2 changes: 1 addition & 1 deletion src/path.hpp
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Expand Up @@ -345,7 +345,7 @@ bool adjacent_mappings(const Mapping& m1, const Mapping& m2);
// Return true if a mapping is a perfect match (i.e. contains no non-match edits)
bool mapping_is_match(const Mapping& m);
double divergence(const Mapping& m);
// Return the identity for the path: perfect matches over total length.
// Return the identity for the path: perfect matches over total length, ignoring soft clips.
// For zero-length paths, returns 0.
double identity(const Path& path);
// compare the agreement between two alignments
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