Skip to content

fix(index): collapse per-node syncmer change record to one entry per position #119

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
AlanZhangUCSC merged 3 commits into from
Jul 15, 2026
Merged

fix(index): collapse per-node syncmer change record to one entry per position #119

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
38b3703
fix(index): collapse per-node syncmer change record to one entry per …
amkram Jul 13, 2026
b77967f
Refactor comments
amkram Jul 14, 2026
fef79c9
Simplify comments
amkram Jul 14, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
40 changes: 40 additions & 0 deletions src/index_single_mode.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
#include <bitset>
#include <chrono>
#include <atomic>
#include <unordered_map>
#include <mutex>
#include <iomanip>
#include <utility>
Expand Down Expand Up @@ -697,6 +698,43 @@ index_single_mode::IndexBuilder::computeNewKminmerRanges(
return newKminmerRanges;
}

namespace {
// Collapse a node's change record to one net entry per position, to handle a node that both edits a
// seed and deletes that seed's block.
void dedupeSyncmerChangeRecord(
std::vector<std::tuple<uint64_t, panmapUtils::seedChangeType, seeding::rsyncmer_t>>& rec,
const index_single_mode::SyncmerSet& finalMap) {
if (rec.size() < 2) return;
std::unordered_map<uint64_t, std::pair<panmapUtils::seedChangeType, seeding::rsyncmer_t>> firstTouch;
firstTouch.reserve(rec.size());
std::vector<uint64_t> order;
order.reserve(rec.size());
bool anyRepeat = false;
for (const auto& [pos, type, rsync] : rec) {
auto [it, inserted] = firstTouch.try_emplace(pos, type, rsync);
if (inserted)
order.push_back(pos);
else
anyRepeat = true;
}
if (!anyRepeat) return;
std::vector<std::tuple<uint64_t, panmapUtils::seedChangeType, seeding::rsyncmer_t>> out;
out.reserve(order.size());
for (uint64_t pos : order) {
const auto& [firstType, firstRsync] = firstTouch[pos];
const bool finalHas = finalMap.find(pos) != finalMap.end();
if (firstType == panmapUtils::seedChangeType::ADD) { // parent lacked pos; keep only if it survives
if (finalHas) out.emplace_back(pos, panmapUtils::seedChangeType::ADD, seeding::rsyncmer_t());
} else { // parent had pos; restore its pre-node value
out.emplace_back(pos,
finalHas ? panmapUtils::seedChangeType::SUB : panmapUtils::seedChangeType::DEL,
firstRsync);
}
}
rec = std::move(out);
}
} // namespace

void index_single_mode::IndexBuilder::buildIndexHelper(panmanUtils::Node* node,
std::unordered_set<std::string_view>& emptyNodes,
panmapUtils::BlockSequences& blockSequences,
Expand Down Expand Up @@ -929,6 +967,7 @@ void index_single_mode::IndexBuilder::buildIndexHelper(panmanUtils::Node* node,
}
}

dedupeSyncmerChangeRecord(refOnSyncmersChangeRecord, refOnSyncmersMap);
std::vector<std::pair<index_single_mode::SyncmerSet::iterator, index_single_mode::SyncmerSet::iterator>>
newKminmerRanges = computeNewKminmerRanges(refOnSyncmersChangeRecord, dfsIndex);

Expand Down Expand Up @@ -1916,6 +1955,7 @@ void index_single_mode::IndexBuilder::processNode(panmanUtils::Node* node,
std::vector<uint64_t> addedSeedHashes;
std::vector<std::pair<uint64_t, uint64_t>> substitutedSeedHashes; // <oldHash, newHash>

dedupeSyncmerChangeRecord(refOnSyncmersChangeRecord, state.refOnSyncmersMap);
std::vector<std::pair<index_single_mode::SyncmerSet::iterator, index_single_mode::SyncmerSet::iterator>>
newKminmerRanges = computeNewKminmerRanges(refOnSyncmersChangeRecord, state, dfsIndex);

Expand Down
43 changes: 42 additions & 1 deletion src/mgsr.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
#include <tbb/enumerable_thread_specific.h>
#include <random>
#include <numeric>
#include <unordered_map>
#include <algorithm>
#include <stack>
#include <bitset>
Expand Down Expand Up @@ -3259,6 +3260,42 @@ std::vector<panmapUtils::NewSyncmerRange> mgsr::mgsrIndexBuilder::computeNewSync
return newSyncmerRanges;
}

namespace {
// Collapse a node's change record to one net entry per position
void dedupeSyncmerChangeRecord(
std::vector<std::tuple<uint64_t, panmapUtils::seedChangeType, seeding::rsyncmer_t>>& rec,
const std::set<uint64_t>& finalMap) {
if (rec.size() < 2) return;
std::unordered_map<uint64_t, std::pair<panmapUtils::seedChangeType, seeding::rsyncmer_t>> firstTouch;
firstTouch.reserve(rec.size());
std::vector<uint64_t> order;
order.reserve(rec.size());
bool anyRepeat = false;
for (const auto& [pos, type, rsync] : rec) {
auto [it, inserted] = firstTouch.try_emplace(pos, type, rsync);
if (inserted)
order.push_back(pos);
else
anyRepeat = true;
}
if (!anyRepeat) return;
std::vector<std::tuple<uint64_t, panmapUtils::seedChangeType, seeding::rsyncmer_t>> out;
out.reserve(order.size());
for (uint64_t pos : order) {
const auto& [firstType, firstRsync] = firstTouch[pos];
const bool finalHas = finalMap.find(pos) != finalMap.end();
if (firstType == panmapUtils::seedChangeType::ADD) {
if (finalHas) out.emplace_back(pos, panmapUtils::seedChangeType::ADD, seeding::rsyncmer_t());
} else {
out.emplace_back(pos,
finalHas ? panmapUtils::seedChangeType::SUB : panmapUtils::seedChangeType::DEL,
firstRsync);
}
}
rec = std::move(out);
}
} // namespace

std::vector<std::pair<std::set<uint64_t>::iterator, std::set<uint64_t>::iterator>>
mgsr::mgsrIndexBuilder::computeNewKminmerRanges(
std::vector<std::tuple<uint64_t, panmapUtils::seedChangeType, seeding::rsyncmer_t>>& refOnSyncmersChangeRecord,
Expand Down Expand Up @@ -3584,6 +3621,9 @@ void mgsr::mgsrIndexBuilder::buildIndexHelper(panmanUtils::Node* node,
if (oldExists && !newExists) {
if (blockOnSyncmers.find(blockId) != blockOnSyncmers.end()) {
for (uint64_t pos : blockOnSyncmers[blockId]) {
// Skip: this position was already deleted earlier in this node (its
// blockOnSyncmers cleanup is deferred), so refOnSyncmers is nullopt here.
if (!refOnSyncmers[pos].has_value()) continue;
refOnSyncmersChangeRecord.emplace_back(
pos, panmapUtils::seedChangeType::DEL, refOnSyncmers[pos].value());
blockOnSyncmersChangeRecord.emplace_back(blockId, pos, panmapUtils::seedChangeType::DEL);
Expand All @@ -3596,6 +3636,7 @@ void mgsr::mgsrIndexBuilder::buildIndexHelper(panmanUtils::Node* node,
}
}

dedupeSyncmerChangeRecord(refOnSyncmersChangeRecord, refOnSyncmersMap);
std::vector<std::pair<std::set<uint64_t>::iterator, std::set<uint64_t>::iterator>> newKminmerRanges =
computeNewKminmerRanges(refOnSyncmersChangeRecord, dfsIndex);

Expand Down Expand Up @@ -8264,4 +8305,4 @@ std::vector<mgsr::MgsrLiteNode*> mgsr::getNearestNodes(mgsr::MgsrLiteNode* node,
}

return result;
}
}
Loading