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Use option to not store nested distances
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@xchang1
xchang1 committed Nov 27, 2024
1 parent def1c35 commit 507aa3a
Showing 1 changed file with 31 additions and 18 deletions.
49 changes: 31 additions & 18 deletions bdsg/src/snarl_distance_index.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -5457,7 +5457,7 @@ SnarlDistanceIndex::SnarlRecordWriter SnarlDistanceIndex::ChainRecordWriter::add
#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);
assert(SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset))== DISTANCED_TRIVIAL_SNARL || SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset))== TRIVIAL_SNARL);
#endif


Expand Down Expand Up @@ -5490,7 +5490,7 @@ SnarlDistanceIndex::SimpleSnarlRecordWriter SnarlDistanceIndex::ChainRecordWrite
size_t snarl_record_size = SIMPLE_SNARL_RECORD_SIZE + 2*snarl_size;
#ifdef debug_distance_indexing
cerr << (*records)->size() << " Adding simple snarl to the end of the array " << endl;
assert(SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset))== DISTANCED_TRIVIAL_SNARL);
assert(SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset))== DISTANCED_TRIVIAL_SNARL || SnarlDistanceIndex::get_record_type((*records)->at(previous_child_offset))== TRIVIAL_SNARL);
#endif


Expand Down Expand Up @@ -6143,10 +6143,12 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
#endif
record_to_offset.emplace(make_pair(temp_index_i,current_record_index), snarl_tree_records->size());

bool ignore_distances = (snarl_size_limit == 0) || (only_top_level_chain_distances && temp_chain_record.tree_depth != 0);

ChainRecordWriter chain_record_constructor;

if (temp_chain_record.chain_components.back() == 0 || snarl_size_limit == 0) {
record_t record_type = snarl_size_limit == 0 ? CHAIN : DISTANCED_CHAIN;
if (temp_chain_record.chain_components.back() == 0 || ignore_distances) {
record_t record_type = ignore_distances ? CHAIN : DISTANCED_CHAIN;
chain_record_constructor = ChainRecordWriter(snarl_tree_records->size(), record_type,
temp_chain_record.prefix_sum.size(), &snarl_tree_records);
chain_record_constructor.set_start_end_connected();
Expand All @@ -6156,7 +6158,7 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
}
chain_record_constructor.set_parent_record_offset(
record_to_offset[make_pair(temp_index_i, temp_chain_record.parent)]);
if (snarl_size_limit != 0) {
if (!ignore_distances) {
chain_record_constructor.set_distance_left_start(temp_chain_record.distance_left_start);
chain_record_constructor.set_distance_right_start(temp_chain_record.distance_right_start);
chain_record_constructor.set_distance_left_end(temp_chain_record.distance_left_end);
Expand Down Expand Up @@ -6187,7 +6189,7 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
}


if (snarl_size_limit != 0) {
if (!ignore_distances) {
chain_record_constructor.set_min_length(temp_chain_record.min_length);
chain_record_constructor.set_max_length(temp_chain_record.max_length);
}
Expand Down Expand Up @@ -6227,7 +6229,7 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
temp_chain_record.backward_loops[chain_node_i], temp_chain_record.chain_components[chain_node_i],
temp_chain_record.max_prefix_sum[chain_node_i],
last_child_offset.first, last_child_was_nontrivial_snarl,
snarl_size_limit != 0);
!ignore_distances);

//Remember this node as the last thing in the chain
last_child_offset = make_pair(new_offset, false);
Expand Down Expand Up @@ -6262,7 +6264,9 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist

//Add the snarl to the chain, and get back the record to fill it in

record_t record_type = snarl_size_limit == 0 ? SNARL :
bool ignore_distances = (snarl_size_limit == 0) || only_top_level_chain_distances;

record_t record_type = ignore_distances ? SNARL :
(temp_snarl_record.node_count < snarl_size_limit ? DISTANCED_SNARL : OVERSIZED_SNARL);
SnarlRecordWriter snarl_record_constructor =
chain_record_constructor.add_snarl(temp_snarl_record.node_count, record_type, last_child_offset.first);
Expand All @@ -6271,7 +6275,7 @@ 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
if (snarl_size_limit != 0) {
if (!ignore_distances) {
snarl_record_constructor.set_min_length(temp_snarl_record.min_length);
snarl_record_constructor.set_max_length(temp_snarl_record.max_length);
}
Expand All @@ -6284,7 +6288,7 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
pair<size_t, size_t> node_rank2 = it.first.second;
const size_t distance = it.second;

if (snarl_size_limit != 0) {
if (!ignore_distances) {
//If we are keeping track of distances
//If the distance exceeded the limit, then it wasn't found in the first place
snarl_record_constructor.set_distance(node_rank1.first, node_rank1.second,
Expand Down Expand Up @@ -6361,16 +6365,17 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
//Make a simple snarl

//Add the snarl to the chain, and get back the record to fill it in
bool ignore_distances = (snarl_size_limit == 0) || only_top_level_chain_distances;

record_t record_type = snarl_size_limit == 0 ? SIMPLE_SNARL : DISTANCED_SIMPLE_SNARL;
record_t record_type = ignore_distances ? SIMPLE_SNARL : DISTANCED_SIMPLE_SNARL;
SimpleSnarlRecordWriter snarl_record_constructor =
chain_record_constructor.add_simple_snarl(temp_snarl_record.node_count, record_type, last_child_offset.first);

//Record how to find the new snarl record
record_to_offset.emplace(make_pair(temp_index_i, child_record_index), snarl_record_constructor.record_offset);

//Fill in snarl info
if (snarl_size_limit != 0) {
if (!ignore_distances) {
snarl_record_constructor.set_min_length(temp_snarl_record.min_length);
snarl_record_constructor.set_max_length(temp_snarl_record.max_length);
}
Expand Down Expand Up @@ -6423,12 +6428,16 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
const TemporaryDistanceIndex::TemporaryNodeRecord& temp_node_record =
temp_index->temp_node_records[temp_chain_record.children[0].second-min_node_id];

record_t record_type = snarl_size_limit == 0 ? NODE : DISTANCED_NODE;

//TODO: I don't think we ever need distances if its a top-level chain distance only index but it doesn't change much
bool ignore_distances = (snarl_size_limit == 0) || (only_top_level_chain_distances && temp_chain_record.tree_depth != 0);

record_t record_type = ignore_distances ? NODE : DISTANCED_NODE;
NodeRecordWriter node_record(snarl_tree_records->size(), 0, record_type, &snarl_tree_records, temp_node_record.node_id);
node_record.set_node_id(temp_node_record.node_id);
node_record.set_rank_in_parent(temp_chain_record.rank_in_parent);
node_record.set_parent_record_offset(record_to_offset[make_pair(temp_index_i, temp_chain_record.parent)]);
if (snarl_size_limit != 0) {
if (!ignore_distances) {
node_record.set_node_length(temp_node_record.node_length);
node_record.set_distance_left_start(temp_chain_record.distance_left_start);
node_record.set_distance_right_start(temp_chain_record.distance_right_start);
Expand All @@ -6444,8 +6453,10 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
cerr << " this is a root-level snarl "
<< temp_index->structure_start_end_as_string(current_record_index) << endl;
#endif

bool ignore_distances = (snarl_size_limit == 0) || only_top_level_chain_distances;
//This is a root-level snarl
record_t record_type = snarl_size_limit == 0 ? ROOT_SNARL : DISTANCED_ROOT_SNARL;
record_t record_type = ignore_distances ? ROOT_SNARL : DISTANCED_ROOT_SNARL;

const TemporaryDistanceIndex::TemporarySnarlRecord& temp_snarl_record = temp_index->temp_snarl_records[current_record_index.second];
record_to_offset.emplace(make_pair(temp_index_i,current_record_index), snarl_tree_records->size());
Expand All @@ -6457,7 +6468,7 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist

//Add distances and record connectivity

if (snarl_size_limit != 0 ) {
if (!ignore_distances ) {


for (const auto& it : temp_snarl_record.distances) {
Expand Down Expand Up @@ -6497,13 +6508,15 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
#endif
const TemporaryDistanceIndex::TemporaryNodeRecord& temp_node_record =
temp_index->temp_node_records[current_record_index.second-min_node_id];
record_t record_type = snarl_size_limit == 0 ? NODE : DISTANCED_NODE;

bool ignore_distances = (snarl_size_limit == 0) || only_top_level_chain_distances;
record_t record_type = ignore_distances ? NODE : DISTANCED_NODE;
NodeRecordWriter node_record(snarl_tree_records->size(), 0, record_type, &snarl_tree_records, temp_node_record.node_id);
node_record.set_node_id(temp_node_record.node_id);
node_record.set_rank_in_parent(temp_node_record.rank_in_parent);
node_record.set_parent_record_offset(record_to_offset[make_pair(temp_index_i, temp_node_record.parent)]);

if (snarl_size_limit != 0) {
if (!ignore_distances) {
node_record.set_node_length(temp_node_record.node_length);
node_record.set_distance_left_start(temp_node_record.distance_left_start);
node_record.set_distance_right_start(temp_node_record.distance_right_start);
Expand Down

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