From d04e0ad44dc7f2f60cc4a84729af44455240126d Mon Sep 17 00:00:00 2001
From: oboulle <olivier.boulle@inria.fr>
Date: Mon, 10 Jun 2024 17:34:24 +0200
Subject: [PATCH] added option to chose matrix or graph on run
---
partitioning/partitioning.cpp | 26 +++++++++++++++++---------
1 file changed, 17 insertions(+), 9 deletions(-)
diff --git a/partitioning/partitioning.cpp b/partitioning/partitioning.cpp
index d84efe6..742de42 100755
--- a/partitioning/partitioning.cpp
+++ b/partitioning/partitioning.cpp
@@ -238,14 +238,18 @@ void minlist_to_csv(const std::vector<std::vector<int>>& minimizer_list, int rea
int main(int argc, char* argv[]) {
// Check if the input and output file paths are provided as arguments
- if (argc != 3) {
- std::cerr << "Usage: " << argv[0] << " <input_fastq> <output_file>" << std::endl;
+ if (argc != 4) {
+ std::cerr << "Usage: " << argv[0] << " <input_fastq> <output_file> [--graph|--matrix]" << std::endl;
return 1;
}
// Get the input and output file paths from the arguments
std::string input_fastq = argv[1];
std::string output_file = argv[2];
+ std::string option = argv[3];
+
+ // Extract the minimizers from the input file
+ std::vector<std::vector<int>> minimizer_list = get_minimizers(input_fastq);
// get the number of sequences from the fastq
std::ifstream file(input_fastq);
@@ -258,13 +262,17 @@ int main(int argc, char* argv[]) {
}
}
- // Extract the minimizers from the input file
- std::vector<std::vector<int>> minimizer_list = get_minimizers(input_fastq);
-
- // Write the minimizer matrix to the output file in CSV format
- //minlist_to_csv(minimizer_list, seq_number, output_file);
-
- minlist_to_graph(minimizer_list, seq_number, output_file);
+ // Call the appropriate function based on the option
+ if (option == "--graph") {
+ minlist_to_graph(minimizer_list, seq_number, output_file);
+ std::cout << "Minimizer graph written to " << output_file << std::endl;
+ } else if (option == "--matrix") {
+ minlist_to_csv(minimizer_list, seq_number, output_file);
+ std::cout << "Minimizer matrix written to " << output_file << std::endl;
+ } else {
+ std::cerr << "Invalid option: " << option << std::endl;
+ return 1;
+ }
return 0;
}
--
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