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Group fix #317

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merged 2 commits into from
Feb 6, 2025
Merged

Group fix #317

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24ad450
refactor: Use rfind() for delimiter-based sequence grouping
ekg Feb 6, 2025
d4661da
chore: Comment out debug output in sequenceIds.hpp
ekg Feb 6, 2025
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12 changes: 9 additions & 3 deletions src/map/include/sequenceIds.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -111,8 +111,8 @@ class SequenceIdManager {
}

if (groupKey.empty() && !prefixDelim.empty()) {
// Use prefix before delimiter as group key
size_t pos = seqName.find(prefixDelim);
// Use prefix before last delimiter as group key
size_t pos = seqName.rfind(prefixDelim);
if (pos != std::string::npos) {
groupKey = seqName.substr(0, pos);
}
Expand All @@ -128,7 +128,13 @@ class SequenceIdManager {
}
metadata[originalIndex].groupId = groupMap[groupKey];
}

/*
// Debug output to verify grouping
for (size_t i = 0; i < metadata.size(); ++i) {
std::cerr << "[DEBUG group assignment] seq " << metadata[i].name
<< " → group " << metadata[i].groupId << std::endl;
}
*/
if (totalSeqs == 0) {
std::cerr << "[SequenceIdManager::buildRefGroups] ERROR: No sequences indexed!" << std::endl;
exit(1);
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