From c786c7df0177e475ef4cffbe46109591ba6690b5 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Wed, 25 Oct 2023 19:27:49 -0500
Subject: [PATCH] fix seg faul on extracted graphs
---
src/subcommand/paths_main.cpp | 33 ++++++++++++++++++++++++---------
1 file changed, 24 insertions(+), 9 deletions(-)
diff --git a/src/subcommand/paths_main.cpp b/src/subcommand/paths_main.cpp
index a8e0aa86..410d9eec 100644
--- a/src/subcommand/paths_main.cpp
+++ b/src/subcommand/paths_main.cpp
@@ -115,6 +115,23 @@ int main_paths(int argc, char** argv) {
}
}
+ const uint64_t shift = graph.min_node_id();
+ std::cerr << "graph.min_node_id() " << graph.min_node_id() << std::endl;
+ std::cerr << "graph.max_node_id() " << graph.max_node_id() << std::endl;
+ std::cerr << "graph.get_node_count() " << graph.get_node_count() << std::endl;
+ std::cerr << "graph.max_node_id() - shift " << (graph.max_node_id() - shift) << std::endl;
+ if (
+ args::get(haplo_matrix) ||
+ (non_reference_nodes && !args::get(non_reference_nodes).empty()) ||
+ (non_reference_ranges && !args::get(non_reference_ranges).empty())
+ ) {
+ // Check if the node IDs are compacted
+ if (graph.max_node_id() - shift >= graph.get_node_count()){
+ std::cerr << "[odgi::paths] error: the node IDs are not compacted. Please run 'odgi sort' using -O, --optimize to optimize the graph." << std::endl;
+ exit(1);
+ }
+ }
+
if (list_path_start_end && list_names) {
std::vector<path_handle_t> paths;
graph.for_each_path_handle([&](const path_handle_t& p) {
@@ -204,13 +221,18 @@ int main_paths(int argc, char** argv) {
uint64_t path_length = 0;
uint64_t path_step_count = 0;
std::vector<uint64_t> row(graph.get_node_count());
+ // Initialize first to avoid possible bugs later
+ for (uint32_t i = 0; i < graph.get_node_count(); ++i) {
+ row[i] = 0;
+ }
+
graph.for_each_step_in_path(
p,
[&](const step_handle_t& s) {
const handle_t& h = graph.get_handle_of_step(s);
path_length += graph.get_length(h);
++path_step_count;
- row[graph.get_id(h)-1]++;
+ row[graph.get_id(h)-shift]++;
});
if (delim) {
std::cout << group_name << "\t";
@@ -220,7 +242,7 @@ int main_paths(int argc, char** argv) {
<< path_step_count;
if (node_length_scale) {
for (uint64_t i = 0; i < row.size(); ++i) {
- std::cout << "\t" << row[i] * graph.get_length(graph.get_handle(i+1));
+ std::cout << "\t" << row[i] * graph.get_length(graph.get_handle(i+shift));
}
} else {
for (uint64_t i = 0; i < row.size(); ++i) {
@@ -361,13 +383,6 @@ int main_paths(int argc, char** argv) {
(non_reference_ranges && !args::get(non_reference_ranges).empty())
) {
const uint64_t min_size_in_bp = min_size ? args::get(min_size) : 0;
-
- // Check if the node IDs are compacted
- const uint64_t shift = graph.min_node_id();
- if (graph.max_node_id() - shift >= graph.get_node_count()){
- std::cerr << "[odgi::paths] error: the node IDs are not compacted. Please run 'odgi sort' using -O, --optimize to optimize the graph." << std::endl;
- exit(1);
- }
// Read paths to use as reference paths
std::vector<path_handle_t> reference_paths;