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add --snarl-outlier option
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@glennhickey
glennhickey committed Dec 19, 2024
1 parent 62b3be2 commit a3b57fa
Showing 1 changed file with 83 additions and 19 deletions.
102 changes: 83 additions & 19 deletions src/subcommand/stats_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
#include "../io/save_handle_graph.hpp"
#include "../gbzgraph.hpp"
#include "../traversal_finder.hpp"
#include "../traversal_clusters.hpp"

using namespace std;
using namespace vg;
Expand Down Expand Up @@ -66,7 +67,8 @@ void help_stats(char** argv) {
<< " -O, --overlap-all print overlap table for the cartesian product of paths" << endl
<< " -R, --snarls print statistics for each snarl" << endl
<< " --snarl-contents print out a table of <snarl, depth, parent, contained node ids>" << endl
<< " --snarl-sample print out reference coordinates on given sample" << endl
<< " --snarl-sample S print out reference coordinates on given sample S" << endl
<< " --snarl-outlier print most diverged path from reference (--snarl-sample required)" << endl
<< " -C, --chains print statistics for each chain" << endl
<< " -F, --format graph format from {VG-Protobuf, PackedGraph, HashGraph, XG}. " <<
"Can't detect Protobuf if graph read from stdin" << endl
Expand Down Expand Up @@ -109,13 +111,15 @@ int main_stats(int argc, char** argv) {
bool chain_stats = false;
bool snarl_contents = false;
string snarl_sample;
bool snarl_outlier = false;
bool format = false;
bool degree_dist = false;
string distance_index_filename;

// Long options with no corresponding short options.
constexpr int OPT_SNARL_CONTENTS = 1000;
constexpr int OPT_SNARL_SAMPLE = 1001;
constexpr int OPT_SNARL_OUTLIER = 1002;
constexpr int64_t snarl_search_context = 100;

int c;
Expand Down Expand Up @@ -146,6 +150,7 @@ int main_stats(int argc, char** argv) {
{"snarls", no_argument, 0, 'R'},
{"snarl-contents", no_argument, 0, OPT_SNARL_CONTENTS},
{"snarl-sample", required_argument, 0, OPT_SNARL_SAMPLE},
{"snarl-outlier", no_argument, 0, OPT_SNARL_OUTLIER},
{"chains", no_argument, 0, 'C'},
{"format", no_argument, 0, 'F'},
{"degree-dist", no_argument, 0, 'D'},
Expand Down Expand Up @@ -251,6 +256,10 @@ int main_stats(int argc, char** argv) {
case OPT_SNARL_SAMPLE:
snarl_sample = optarg;
break;

case OPT_SNARL_OUTLIER:
snarl_outlier = true;
break;

case 'C':
chain_stats = true;
Expand Down Expand Up @@ -297,6 +306,11 @@ int main_stats(int argc, char** argv) {
exit(1);
}

if (snarl_outlier && snarl_sample.empty()) {
cerr << "error [vg stats]: --snarl-outlier can only be used with --snarl-sample" << endl;
exit(1);
}

bdsg::ReferencePathOverlayHelper overlay_helper;
unique_ptr<PathHandleGraph> path_handle_graph;
PathHandleGraph* graph = nullptr;
Expand Down Expand Up @@ -1142,18 +1156,24 @@ int main_stats(int argc, char** argv) {
if (!snarl_sample.empty()) {
// optionally prefix with bed-like refpath coordinates if --snarl-sample given
cout <<"Contig\tStartPos\tEndPos\t";
if (snarl_outlier) {
cout << "OutlierName\tOutlierJaccard\tOutlierLen\t";
}

if (pp_graph == nullptr) {
pp_graph = overlay_helper.apply(graph);
}
vector<string> ref_path_names;
pp_graph->for_each_path_of_sample(snarl_sample, [&](path_handle_t path_handle) {
ref_path_names.push_back(graph->get_path_name(path_handle));
ref_path_names.push_back(pp_graph->get_path_name(path_handle));
});
if (ref_path_names.empty()) {
cerr << "error [vg stats]: unable to find any paths of --snarl-sample " << snarl_sample << endl;
exit(1);
}
if (snarl_outlier) {
ref_path_names.clear(); // if searching for outliers, we want all traversals
}
path_trav_finder = unique_ptr<PathTraversalFinder>(new PathTraversalFinder(*pp_graph, ref_path_names));
}
cout << "Start\tStart-Reversed\tEnd\tEnd-Reversed\tUltrabubble\tUnary\tShallow-Nodes\tShallow-Edges\tShallow-bases\tDeep-Nodes\tDeep-Edges\tDeep-Bases\tDepth\tChildren\tChains\tChains-Children\tNet-Graph-Size\n";
Expand All @@ -1164,15 +1184,26 @@ int main_stats(int argc, char** argv) {
if (snarl_stats) {
if (!snarl_sample.empty()) {
// find the reference interval from path index if snarl lies directly on reference path
vector<PathInterval> travs;
std::tie(std::ignore, travs) = path_trav_finder->find_path_traversals(
vector<Traversal> travs;
vector<PathInterval> trav_intervals;
std::tie(travs, trav_intervals) = path_trav_finder->find_path_traversals(
pp_graph->get_handle(snarl->start().node_id(), snarl->start().backward()),
pp_graph->get_handle(snarl->end().node_id(), snarl->end().backward()));
if (travs.empty() && snarl_to_ref.count(manager.parent_of(snarl))) {
for (int64_t i = 0; i < trav_intervals.size(); ++i) {
// make sure ref trav is first
if (pp_graph->get_sample_name(pp_graph->get_path_handle_of_step(trav_intervals[i].first)) == snarl_sample) {
if (i > 1) {
swap(travs[0], travs[1]);
swap(trav_intervals[0], trav_intervals[i]);
}
break;
}
}
if (trav_intervals.empty() && snarl_to_ref.count(manager.parent_of(snarl))) {
// snarl's not on the reference path, us its parent interval
travs.push_back(snarl_to_ref.at(manager.parent_of(snarl)));
trav_intervals.push_back(snarl_to_ref.at(manager.parent_of(snarl)));
}
if (travs.empty()) {
if (trav_intervals.empty()) {
// search toward the reference path
unordered_map<path_handle_t, vector<step_handle_t>> start_steps;
unordered_map<path_handle_t, vector<step_handle_t>> end_steps;
Expand Down Expand Up @@ -1206,43 +1237,43 @@ int main_stats(int argc, char** argv) {
step != graph->path_end(graph->get_path_handle_of_step(start_path_steps.second[0]));
step = graph->get_next_step(step)) {
if (end_ids.count(graph->get_id(graph->get_handle_of_step(step)))) {
travs.push_back(make_pair(start_path_steps.second[0],
trav_intervals.push_back(make_pair(start_path_steps.second[0],
end_ids[graph->get_id(graph->get_handle_of_step(step))]));
break;
}
}
// search backward
if (travs.empty()) {
if (trav_intervals.empty()) {
for (step_handle_t step = graph->get_previous_step(start_path_steps.second[0]);
step != graph->path_front_end(graph->get_path_handle_of_step(start_path_steps.second[0]));
step = graph->get_previous_step(step)) {
if (end_ids.count(graph->get_id(graph->get_handle_of_step(step)))) {
travs.push_back(make_pair(start_path_steps.second[0],
trav_intervals.push_back(make_pair(start_path_steps.second[0],
end_ids[graph->get_id(graph->get_handle_of_step(step))]));
break;
}
}
}
}
if (!travs.empty()) {
if (!trav_intervals.empty()) {
break;
}
}
// unlikely, but maybe only one end of the snarl reaches the reference. in that case
// we just consider it both ends of the interval
if (travs.empty() && !start_steps.empty()) {
travs.push_back(make_pair(start_steps.begin()->second.front(), start_steps.begin()->second.front()));
if (trav_intervals.empty() && !start_steps.empty()) {
trav_intervals.push_back(make_pair(start_steps.begin()->second.front(), start_steps.begin()->second.front()));
}
if (travs.empty() && !end_steps.empty()) {
travs.push_back(make_pair(end_steps.begin()->second.front(), end_steps.begin()->second.front()));
if (trav_intervals.empty() && !end_steps.empty()) {
trav_intervals.push_back(make_pair(end_steps.begin()->second.front(), end_steps.begin()->second.front()));
}
}
if (travs.empty()) {
if (trav_intervals.empty()) {
cout << ".\t.\t.\t";
} else {
// note: in case of a cycle, we're just taking the first found
step_handle_t start_step = travs.front().first;
step_handle_t end_step = travs.front().second;
step_handle_t start_step = trav_intervals.front().first;
step_handle_t end_step = trav_intervals.front().second;
int64_t start_pos = pp_graph->get_position_of_step(start_step);
int64_t end_pos = pp_graph->get_position_of_step(end_step);
if (end_pos < start_pos) {
Expand All @@ -1254,7 +1285,40 @@ int main_stats(int argc, char** argv) {
<< end_pos << "\t";

// use this interval for off-reference children
snarl_to_ref[snarl] = travs.front();
snarl_to_ref[snarl] = trav_intervals.front();

// print the outlier of snarl (only works if snarl is exactly on reference since it
// requires the full traversal list)
if (snarl_outlier) {
int64_t outlier_idx = -1;
double outlier_jaccard = numeric_limits<double>::max();
int64_t outlier_len = -1;
if (trav_intervals.size() > 1) {
vector<double> jaccards(trav_intervals.size());
multiset<handle_t> refset;
for (handle_t handle : travs[0]) {
refset.insert(handle);
}
for (int64_t i = 1; i < trav_intervals.size(); ++i) {
multiset<handle_t> travset;
int64_t travlen = 0;
for (handle_t handle : travs[i]) {
travset.insert(handle);
travlen += pp_graph->get_length(handle);
}
double jaccard = weighted_jaccard_coefficient(pp_graph, refset, travset);
if (jaccard < outlier_jaccard) {
outlier_idx = i;
outlier_jaccard = jaccard;
outlier_len = travlen;
}
}
cout << pp_graph->get_path_name(pp_graph->get_path_handle_of_step(trav_intervals[outlier_idx].first))
<< "\t" << outlier_jaccard << "\t" << outlier_len << "\t";
} else {
cout << ".\t.\t.\t";
}
}
}
}

Expand Down

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vg CI tests complete for branch glenn. View the full report here.

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