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spoa::Graph::GenerateConsensus additional overload #73

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Nov 27, 2023
Merged

spoa::Graph::GenerateConsensus additional overload #73

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4 changes: 4 additions & 0 deletions include/spoa/graph.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,10 @@ class Graph {

std::string GenerateConsensus(std::int32_t min_coverage);

std::string GenerateConsensus(
std::int32_t min_coverage,
std::vector<std::uint32_t> *summary);

std::string GenerateConsensus(
std::vector<std::uint32_t>* summary,
bool verbose = false);
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22 changes: 22 additions & 0 deletions src/graph.cpp
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Expand Up @@ -385,6 +385,28 @@ std::string Graph::GenerateConsensus(std::int32_t min_coverage) {
return dst;
}

std::string Graph::GenerateConsensus(std::int32_t min_coverage,
std::vector<std::uint32_t> *summary) {
if (!summary) {
throw std::invalid_argument(
"[spoa::Graph::GenerateConsensus] error: invalid ptr to summary");
}
summary->clear();

auto dst = GenerateConsensus(min_coverage);
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for (const auto &it : consensus_) {
if (static_cast<std::int32_t>(it->Coverage()) >= min_coverage) {
summary->emplace_back(0);
summary->back() += it->Coverage();
for (const auto &jt : it->aligned_nodes) {
summary->back() += jt->Coverage();
}
}
}

return dst;
}

std::string Graph::GenerateConsensus(
std::vector<std::uint32_t>* summary,
bool verbose) {
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