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Distance bugfix #204

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merged 3 commits into from
Sep 19, 2024
Merged

Distance bugfix #204

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c8a10cb
Fix bug looping in a chain without a snarl
xchang1 Sep 11, 2024
33e2fc2
Don't try to add lengths for a distanceless index
xchang1 Sep 12, 2024
7df2076
Get chain distance properly
xchang1 Sep 12, 2024
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37 changes: 23 additions & 14 deletions bdsg/src/snarl_distance_index.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3179,7 +3179,7 @@ size_t SnarlDistanceIndex::chain_minimum_length(const net_handle_t& net) const {
assert(is_chain(net));
#endif
if (is_trivial_chain(net)) {
return NodeRecord(net, &snarl_tree_records).get_node_length();
return minimum_length(net);
} else {
return ChainRecord(net, &snarl_tree_records).get_min_length();
}
Expand Down Expand Up @@ -4351,7 +4351,7 @@ SnarlDistanceIndex::SimpleSnarlRecordWriter::SimpleSnarlRecordWriter (size_t nod
SimpleSnarlRecord::records = records;

#ifdef debug_distance_indexing
cerr << " Resizing array to add simple snarl: length " << (*records)->size() << " -> " << (*records)->size() + SIM PLE_SNARL_RECORD_SIZE + 2*node_count << endl;
cerr << " Resizing array to add simple snarl: length " << (*records)->size() << " -> " << (*records)->size() + SIMPLE_SNARL_RECORD_SIZE + 2*node_count << endl;
cerr << "\t simple snarl has " << node_count << " nodes " << endl;
#endif
(*records)->resize((*records)->size() + SIMPLE_SNARL_RECORD_SIZE + 2*node_count);
Expand Down Expand Up @@ -4762,7 +4762,7 @@ SnarlDistanceIndex::TrivialSnarlRecordWriter::TrivialSnarlRecordWriter (size_t p
assert (type == TRIVIAL_SNARL || type == DISTANCED_TRIVIAL_SNARL);

#ifdef debug_distance_indexing
cerr << " Resizing array to add trivial snarl: length " << (*records)->size() << " -> " << (*records)->size() + TR IVIAL_SNARL_RECORD_SIZE << endl;
cerr << " Resizing array to add trivial snarl: length " << (*records)->size() << " -> " << (*records)->size() + TRIVIAL_SNARL_RECORD_SIZE << endl;
#endif

if (new_record) {
Expand Down Expand Up @@ -5275,7 +5275,7 @@ SnarlDistanceIndex::ChainRecordWriter::ChainRecordWriter (size_t pointer, record
ChainRecord::record_offset = pointer;
ChainRecord::records = records;
#ifdef debug_distance_indexing
cerr << " Resizing array to add chain: length " << (*records)->size() << " -> " << (*records)->size() + CHAIN_RECO RD_SIZE << endl;
cerr << " Resizing array to add chain: length " << (*records)->size() << " -> " << (*records)->size() + CHAIN_RECORD_SIZE << endl;
#endif
(*records)->resize((*records)->size() + CHAIN_RECORD_SIZE);
set_node_count(node_count);
Expand Down Expand Up @@ -5335,6 +5335,7 @@ SnarlDistanceIndex::SnarlRecordWriter SnarlDistanceIndex::ChainRecordWriter::add
size_t snarl_record_size = SnarlRecord::record_size(type, snarl_size);
#ifdef debug_distance_indexing
cerr << (*records)->size() << " Adding child snarl length to the end of the array " << endl;
cerr << "Previous child was at " << previous_child_offset << endl;
assert(SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset))== DISTANCED_TRIVIAL_SNARL);
#endif

Expand Down Expand Up @@ -5403,9 +5404,10 @@ size_t SnarlDistanceIndex::ChainRecordWriter::add_node(nid_t node_id, size_t nod
#ifdef debug_distance_indexing
cerr << "Adding new node to chain, with previous child at offset " << previous_child_offset << endl;
#endif
if (SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset)) == DISTANCED_TRIVIAL_SNARL
if ((SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset)) == DISTANCED_TRIVIAL_SNARL ||
SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset)) == TRIVIAL_SNARL)
&& (TrivialSnarlRecord(previous_child_offset, records).get_node_count() == MAX_TRIVIAL_SNARL_NODE_COUNT
|| new_record)) {
|| new_record || reverse_loop == 0)) {
//If the last thing was a trivial snarl and it is full, then finish it off
(*records)->at(previous_child_offset-1) = TrivialSnarlRecord(previous_child_offset, records).get_record_size();
size_t current_size = (*records)->size();
Expand All @@ -5414,6 +5416,7 @@ size_t SnarlDistanceIndex::ChainRecordWriter::add_node(nid_t node_id, size_t nod
}

if (previous_child_offset == 0
|| SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset)) == SNARL
|| SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset)) == DISTANCED_SNARL
|| SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset)) == OVERSIZED_SNARL
|| SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset)) == DISTANCED_SIMPLE_SNARL
Expand Down Expand Up @@ -6039,8 +6042,10 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
}


chain_record_constructor.set_min_length(temp_chain_record.min_length);
chain_record_constructor.set_max_length(temp_chain_record.max_length);
if (snarl_size_limit != 0) {
chain_record_constructor.set_min_length(temp_chain_record.min_length);
chain_record_constructor.set_max_length(temp_chain_record.max_length);
}
chain_record_constructor.set_rank_in_parent(temp_chain_record.rank_in_parent);
chain_record_constructor.set_start_node(temp_chain_record.start_node_id, temp_chain_record.start_node_rev);
chain_record_constructor.set_end_node(temp_chain_record.end_node_id, temp_chain_record.end_node_rev);
Expand Down Expand Up @@ -6120,8 +6125,10 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
record_to_offset.emplace(make_pair(temp_index_i, child_record_index), snarl_record_constructor.record_offset);

//Fill in snarl info
snarl_record_constructor.set_min_length(temp_snarl_record.min_length);
snarl_record_constructor.set_max_length(temp_snarl_record.max_length);
if (snarl_size_limit != 0) {
snarl_record_constructor.set_min_length(temp_snarl_record.min_length);
snarl_record_constructor.set_max_length(temp_snarl_record.max_length);
}
snarl_record_constructor.set_distance_start_start(temp_snarl_record.distance_start_start);
snarl_record_constructor.set_distance_end_end(temp_snarl_record.distance_end_end);

Expand Down Expand Up @@ -6217,8 +6224,10 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
record_to_offset.emplace(make_pair(temp_index_i, child_record_index), snarl_record_constructor.record_offset);

//Fill in snarl info
snarl_record_constructor.set_min_length(temp_snarl_record.min_length);
snarl_record_constructor.set_max_length(temp_snarl_record.max_length);
if (snarl_size_limit != 0) {
snarl_record_constructor.set_min_length(temp_snarl_record.min_length);
snarl_record_constructor.set_max_length(temp_snarl_record.max_length);
}

//Add the children of the simple snarl
for (size_t i = 0 ; i < temp_snarl_record.node_count ; i++ ) {
Expand Down Expand Up @@ -6460,8 +6469,8 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
#ifdef debug_distance_indexing
cerr << " child " << temp_index->structure_start_end_as_string(child) << endl;
cerr << " " << child.first << " " << child.second << endl;
cerr << " Add child " << net_handle_as_string(get_net_handle_from_values(record_to_offset[make_pair(temp_index_i, child)], START_END))
<< " at offset " << record_to_offset[make_pair(temp_index_i, child)]
//cerr << " Add child " << net_handle_as_string(get_net_handle_from_values(record_to_offset[make_pair(temp_index_i, child)], START_END))
cerr << " at offset " << record_to_offset[make_pair(temp_index_i, child)]
<< " to child list at offset " << snarl_tree_records->size() << endl;
#endif
}
Expand Down
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