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minor efficiency improvements and code cleanup #501

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minor efficiency improvements and code cleanup #501

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12dafa2
optimize EC intersection and shading map lookups
svdrecbd Jan 30, 2026
3e64534
implement lazy allocation for shading map to eliminate common-case ov…
svdrecbd Jan 30, 2026
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2 changes: 1 addition & 1 deletion ext/bifrost/src/DataStorage.tcc
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ DataStorage<U>::DataStorage(const DataStorage& o) : color_sets(nullptr), shared_

unitig_cs_link = new std::atomic<uint64_t>[sz_link];

for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load();
}

if ((o.data != nullptr) && (o.sz_cs != 0)){
Expand Down
26 changes: 19 additions & 7 deletions src/KmerIndex.cpp
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Expand Up @@ -381,14 +381,21 @@ void KmerIndex::BuildTranscripts(const ProgramOptions& opt, std::ofstream& out)
target_names_.push_back(name);

// Begin Shading
if (!shadeToColorTranscriptMap.empty()) {
shadeToColorTranscriptMap.push_back(-1);
}
auto shade_info = shadedTargetName(name);
if (shade_info.first != "") {
std::string tname = shade_info.first;
std::string variant = shade_info.second;
auto it = std::find(target_names_.begin(), target_names_.end(), tname);
if (it != target_names_.end()) {
shadeToColorTranscriptMap[target_names_.size() - 1] =
if (shadeToColorTranscriptMap.empty()) {
shadeToColorTranscriptMap.resize(target_names_.size(), -1);
}
shadeToColorTranscriptMap.back() =
std::distance(target_names_.begin(), it);
num_shades++;
}
}
// End Shading
Expand Down Expand Up @@ -1134,8 +1141,7 @@ void KmerIndex::BuildEquivalenceClasses(const ProgramOptions& opt, const std::st

trinfos[n->id].push_back(tr);
// Begin Shading
auto it = shadeToColorTranscriptMap.find(tr.trid);
if (it != shadeToColorTranscriptMap.end()) {
if (tr.trid < shadeToColorTranscriptMap.size() && shadeToColorTranscriptMap[tr.trid] != -1) {
tr.trid = shadeToColorTranscriptMap[tr.trid];
trinfos[n->id].push_back(tr); // Add the color of the original transcript as well
}
Expand Down Expand Up @@ -1168,8 +1174,8 @@ void KmerIndex::BuildEquivalenceClasses(const ProgramOptions& opt, const std::st
std::cerr << "[build] target de Bruijn graph has " << dbg.size() << " contigs and contains "
<< dbg.nbKmers() << " k-mers " << std::endl;
// Begin Shading
if (shadeToColorTranscriptMap.size() != 0) {
std::cerr << "[build] number of shades: " << std::to_string(shadeToColorTranscriptMap.size())
if (num_shades != 0) {
std::cerr << "[build] number of shades: " << std::to_string(num_shades)
<< std::endl;
}
// End Shading
Expand Down Expand Up @@ -1550,6 +1556,8 @@ void KmerIndex::load(ProgramOptions& opt, bool loadKmerTable, bool loadDlist) {
// 6. read in target ids
target_names_.clear();
target_names_.reserve(num_trans);
shadeToColorTranscriptMap.clear();
num_shades = 0;

size_t bufsz = 1024;
buffer = new char[bufsz];
Expand All @@ -1576,7 +1584,11 @@ void KmerIndex::load(ProgramOptions& opt, bool loadKmerTable, bool loadDlist) {
std::string variant = shade_info.second;
auto it = std::find(target_names_.begin(), target_names_.end(), tname);
if (it != target_names_.end()) {
if (shadeToColorTranscriptMap.empty()) {
shadeToColorTranscriptMap.resize(num_trans, -1);
}
shadeToColorTranscriptMap[i] = std::distance(target_names_.begin(), it);
num_shades++;
}
use_shade = true;
shade_sequences.add(i);
Expand Down Expand Up @@ -1606,8 +1618,8 @@ void KmerIndex::load(ProgramOptions& opt, bool loadKmerTable, bool loadDlist) {
<< std::endl;
}
// Begin Shading
if (shadeToColorTranscriptMap.size() != 0) {
std::cerr << "[build] number of shades: " << std::to_string(shadeToColorTranscriptMap.size())
if (num_shades != 0) {
std::cerr << "[build] number of shades: " << std::to_string(num_shades)
<< std::endl;
}
// End Shading
Expand Down
4 changes: 3 additions & 1 deletion src/KmerIndex.h
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Expand Up @@ -81,6 +81,7 @@ struct KmerIndex {
no_jump = opt.no_jump;
// Begin Shading
use_shade = false;
num_shades = 0;
// End Shading
}

Expand Down Expand Up @@ -155,7 +156,8 @@ struct KmerIndex {

// Begin Shading
// Here, we use the concepts of "shades" as proposed by in Ornaments by Adduri & Kim, 2024 for bias-corrected allele-specific expression estimation
std::unordered_map<int, int> shadeToColorTranscriptMap;
std::vector<int> shadeToColorTranscriptMap;
int num_shades;
Roaring shade_sequences;
bool use_shade;
// End Shading
Expand Down
6 changes: 3 additions & 3 deletions src/MinCollector.cpp
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Expand Up @@ -295,7 +295,7 @@ Roaring MinCollector::modeECs(std::vector<std::pair<const_UnitigMap<Node>, int32
sort(v.begin(), v.end(), [&](const std::pair<const_UnitigMap<Node>, int>& a, const std::pair<const_UnitigMap<Node>, int>& b)
{
if (a.first.isSameReferenceUnitig(b.first) &&
a.first.getData()->ec[a.first.dist] == b.first.getData()->ec[b.first.dist]) {
a.first.getData()->get_mc_contig(a.first.dist).first == b.first.getData()->get_mc_contig(b.first.dist).first) {
return a.second < b.second;
} else {
return a.first.getData()->id < b.first.getData()->id;
Expand Down Expand Up @@ -368,7 +368,7 @@ Roaring MinCollector::intersectECs_long(std::vector<std::pair<const_UnitigMap<No
sort(v.begin(), v.end(), [&](const std::pair<const_UnitigMap<Node>, int>& a, const std::pair<const_UnitigMap<Node>, int>& b)
{
if (a.first.isSameReferenceUnitig(b.first) &&
a.first.getData()->ec[a.first.dist] == b.first.getData()->ec[b.first.dist]) {
a.first.getData()->get_mc_contig(a.first.dist).first == b.first.getData()->get_mc_contig(b.first.dist).first) {
return a.second < b.second;
} else {
return a.first.getData()->id < b.first.getData()->id;
Expand Down Expand Up @@ -436,7 +436,7 @@ Roaring MinCollector::intersectECs(std::vector<std::pair<const_UnitigMap<Node>,
sort(v.begin(), v.end(), [&](const std::pair<const_UnitigMap<Node>, int>& a, const std::pair<const_UnitigMap<Node>, int>& b)
{
if (a.first.isSameReferenceUnitig(b.first) &&
a.first.getData()->ec[a.first.dist] == b.first.getData()->ec[b.first.dist]) {
a.first.getData()->get_mc_contig(a.first.dist).first == b.first.getData()->get_mc_contig(b.first.dist).first) {
return a.second < b.second;
} else {
return a.first.getData()->id < b.first.getData()->id;
Expand Down