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Make distanceless trivial snarls not include node lengths
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@xchang1
xchang1 committed Nov 26, 2024
1 parent 5d12710 commit 85ac4a1
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Showing 2 changed files with 39 additions and 16 deletions.
7 changes: 5 additions & 2 deletions bdsg/include/bdsg/snarl_distance_index.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -821,7 +821,8 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
* [trivial snarl tag, pointer to parent, node count, prefix sum, fd loop, rev loop, component]
* The record is followed by [node id+orientation, right prefix sum] for each node in the trivial snarl
* So the total length of the trivial snarl is 8+2*#nodes
* So the total length of the distanced trivial snarl is 8+2*#nodes, and the length of a distanceless
* trivial snarl is 8+#nodes
* The right prefix sum is the sum from the start of the trivial chain to the right side of the node (relative to the chain)
* The node_record_offset in a net_handle_t to a trivial snarl points to a node in the trivial snarl
Expand Down Expand Up @@ -1144,7 +1145,9 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
bool get_is_reversed_in_parent(size_t node_rank) const; //is the node_rank-th node reversed

size_t get_record_size() {
return TRIVIAL_SNARL_RECORD_SIZE + (get_node_count() * 2);
return get_record_type() == DISTANCED_TRIVIAL_SNARL
? TRIVIAL_SNARL_RECORD_SIZE + (get_node_count() * 2)
: TRIVIAL_SNARL_RECORD_SIZE + get_node_count();
}
TrivialSnarlRecord (size_t offset, const bdsg::yomo::UniqueMappedPointer<bdsg::MappedIntVector>* tree_records);
};
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48 changes: 34 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 @@ -3431,7 +3431,7 @@ size_t SnarlDistanceIndex::SnarlTreeRecord::get_min_length() const {
size_t val;
if (type == DISTANCED_NODE ) {
return (*records)->at(record_offset + NODE_LENGTH_OFFSET);
} else if (type == TRIVIAL_SNARL || type == DISTANCED_TRIVIAL_SNARL) {
} else if (type == DISTANCED_TRIVIAL_SNARL) {
size_t last_node_offset = TrivialSnarlRecord(record_offset, records).get_node_count()-1;
return (*records)->at(record_offset + TRIVIAL_SNARL_RECORD_SIZE + (last_node_offset*2) + 1);
} else if (type == DISTANCED_SNARL || type == OVERSIZED_SNARL) {
Expand All @@ -3456,7 +3456,7 @@ size_t SnarlDistanceIndex::SnarlTreeRecord::get_max_length() const {
size_t val;
if (type == DISTANCED_NODE ) {
return (*records)->at(record_offset + NODE_LENGTH_OFFSET);
} else if (type == TRIVIAL_SNARL || type == DISTANCED_TRIVIAL_SNARL) {
} else if (type == DISTANCED_TRIVIAL_SNARL) {
size_t last_node_offset = TrivialSnarlRecord(record_offset, records).get_node_count()-1;
return (*records)->at(record_offset + TRIVIAL_SNARL_RECORD_SIZE + (last_node_offset*2) + 1);
} else if (type == DISTANCED_SNARL || type == OVERSIZED_SNARL) {
Expand Down Expand Up @@ -4723,10 +4723,14 @@ size_t SnarlDistanceIndex::TrivialSnarlRecord::get_rank_in_parent(size_t node_ra
return record_offset+node_rank;
}
nid_t SnarlDistanceIndex::TrivialSnarlRecord::get_node_id(size_t node_rank) const {
return (*records)->at(record_offset + TRIVIAL_SNARL_RECORD_SIZE + (2*node_rank)) >> 1;
return get_record_type() == TRIVIAL_SNARL
? (*records)->at(record_offset + TRIVIAL_SNARL_RECORD_SIZE + node_rank) >> 1
: (*records)->at(record_offset + TRIVIAL_SNARL_RECORD_SIZE + (2*node_rank)) >> 1;
}
bool SnarlDistanceIndex::TrivialSnarlRecord::get_is_reversed_in_parent(size_t node_rank) const {
return (*records)->at(record_offset + TRIVIAL_SNARL_RECORD_SIZE + (2*node_rank)) & 1;
return get_record_type() == TRIVIAL_SNARL
? (*records)->at(record_offset + TRIVIAL_SNARL_RECORD_SIZE + node_rank) & 1
: (*records)->at(record_offset + TRIVIAL_SNARL_RECORD_SIZE + (2*node_rank)) & 1;
}

SnarlDistanceIndex::NodeRecordWriter::NodeRecordWriter (size_t pointer, size_t node_offset, record_t type,
Expand Down Expand Up @@ -5547,7 +5551,7 @@ size_t SnarlDistanceIndex::ChainRecordWriter::add_node(nid_t node_id, size_t nod


//Create a new trivial snarl record
TrivialSnarlRecordWriter trivial_snarl_record((*records)->size(), DISTANCED_TRIVIAL_SNARL, records, true);
TrivialSnarlRecordWriter trivial_snarl_record((*records)->size(), include_distances ? DISTANCED_TRIVIAL_SNARL : TRIVIAL_SNARL, records, true);
trivial_snarl_record.set_parent_record_offset(record_offset);
trivial_snarl_record.set_node_count(1);
if (include_distances) {
Expand All @@ -5559,15 +5563,26 @@ size_t SnarlDistanceIndex::ChainRecordWriter::add_node(nid_t node_id, size_t nod
trivial_snarl_record.set_chain_component(component);

start_i = (*records)->size();
(*records)->resize(start_i+2);
(*records)->at(start_i) = (node_id<<1) | is_reversed_in_parent;
(*records)->at(start_i+1) = node_length;
if (include_distances) {
(*records)->resize(start_i+2);
(*records)->at(start_i) = (node_id<<1) | is_reversed_in_parent;
(*records)->at(start_i+1) = node_length;
} else {
(*records)->resize(start_i+1);
(*records)->at(start_i) = (node_id<<1) | is_reversed_in_parent;
}
#ifdef debug_distance_indexing
cerr << start_i << " Node in trivial snarl " << ((node_id<<1) | is_reversed_in_parent) << endl;
cerr << start_i +1 << " prefix sum in trivial snarl " << ((*records)->at(start_i-1) + node_length) << endl;
if (get_record_type() == DISTANCED_CHAIN) {
cerr << start_i +1 << " prefix sum in trivial snarl " << ((*records)->at(start_i-1) + node_length) << endl;
}
#endif
#ifdef count_allocations
cerr << "trivial_snarl\t2\t" << (*records)->size() << endl;
if (get_record_type() == DISTANCED_CHAIN) {
cerr << "trivial_snarl\t2\t" << (*records)->size() << endl;
} else {
cerr << "trivial_snarl\t1\t" << (*records)->size() << endl;
}
#endif

//Return the offset offset of the new trivial snarl record
Expand All @@ -5577,9 +5592,14 @@ size_t SnarlDistanceIndex::ChainRecordWriter::add_node(nid_t node_id, size_t nod
//
//Add the node and its right prefix sum
size_t start_i = (*records)->size();
(*records)->resize(start_i+2);
(*records)->at(start_i) = (node_id<<1) | is_reversed_in_parent;
(*records)->at(start_i+1) = (*records)->at(start_i-1) + node_length;
if (include_distances) {
(*records)->resize(start_i+2);
(*records)->at(start_i) = (node_id<<1) | is_reversed_in_parent;
(*records)->at(start_i+1) = (*records)->at(start_i-1) + node_length;
} else {
(*records)->resize(start_i+1);
(*records)->at(start_i) = (node_id<<1) | is_reversed_in_parent;
}
#ifdef debug_distance_indexing
cerr << start_i << " Node in trivial snarl " << ((node_id<<1) | is_reversed_in_parent) << endl;
cerr << start_i +1 << " prefix sum in trivial snarl " << ((*records)->at(start_i-1) + node_length) << endl;
Expand All @@ -5588,7 +5608,7 @@ size_t SnarlDistanceIndex::ChainRecordWriter::add_node(nid_t node_id, size_t nod
cerr << "trivial_snarl\t2\t" << (*records)->size() << endl;
#endif

TrivialSnarlRecordWriter trivial_snarl_record(previous_child_offset, DISTANCED_TRIVIAL_SNARL, records, false);
TrivialSnarlRecordWriter trivial_snarl_record(previous_child_offset, include_distances ? DISTANCED_TRIVIAL_SNARL : TRIVIAL_SNARL, records, false);

//Increment the node count
size_t old_node_count = trivial_snarl_record.get_node_count();
Expand Down

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