changes to data structure

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.22.1)
-project(RNAnue VERSION 0.2.3)
+project(RNAnue VERSION 0.2.4)
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 set(CMAKE_CXX_FLAGS -fopenmp)
@@ -11,7 +11,7 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/include/Config.hpp.in ${CMAKE_CURRENT
 
 ###### SeqAn #####
 list (APPEND CMAKE_PREFIX_PATH "${CMAKE_CURRENT_SOURCE_DIR}/seqan3/build_system")
-find_package (seqan3 3.0 REQUIRED)
+find_package (seqan3 3.3.0 REQUIRED)
 find_package(OpenMP)
 
 ###### Boost ######
@@ -38,6 +38,9 @@ target_link_libraries(RNAnue PkgConfig::HTSLIB)
 cmake_print_properties(TARGETS RNAnue PROPERTIES TARGET_INCLUDE_DIRECTORIES)
 
 ###### Tests ######
+# make tests optional
+option(BUILD_TESTS "Building unit tests" OFF)
+
 file(GLOB TEST_SOURCES "test/*.cpp")
 file(GLOB SOURCES "src/*.cpp")
 list(REMOVE_ITEM SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/src/main.cpp)

include/Utility.hpp

@@ -6,6 +6,7 @@
 #include <iomanip>
 #include <chrono>
 #include <random>
+#include <filesystem>
 
 
 // Boost
@@ -18,6 +19,7 @@
 #include "DataTypes.hpp"
 
 namespace fs = boost::filesystem;
+namespace stdfs = std::filesystem;
 
 // filesystem manipulation
 namespace helper {

src/Data.cpp

@@ -1,6 +1,7 @@
 #include "Data.hpp"
 
 Data::Data(po::variables_map params) : params(params) {
+    std::cout << helper::getTime() << "Data object created\n";
     std::string subcall = params["subcall"].as<std::string>();
     fs::path outDir = fs::path(params["outdir"].as<std::string>());
 
@@ -67,7 +68,7 @@ void Data::detectDataPrep() {
 }
 
 void Data::clusteringDataPrep() {
-fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
+    fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
     fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "detect/trtms";
 
     GroupsPath groups = getGroupsPath(ctrlsPath, trtmsPath);

src/main.cpp

@@ -25,6 +25,27 @@ void showVersion(std::ostream& _str) {
     _str << std::endl;
 }
 
+void makePathAbs(po::variables_map& params, std::string param, fs::path& configFileDir) {
+    if(params.count(param)) {
+        fs::path filePath = fs::path(params[param].as<std::string>());
+        if(filePath.empty()) { return; } // if file path is empty, do nothing
+        if(!filePath.is_absolute()) {
+            fs::path newPath = configFileDir / filePath;
+            params.erase(param); // remove param from variables_map
+            // add corrected path to variables_map
+            params.insert(std::make_pair(param, po::variable_value((configFileDir / filePath).string(), false)));
+        }
+    }
+}
+
+// correct the paths to absolute paths (if they are relative)
+void correctPaths(po::variables_map& params, fs::path& configFileDir) {
+    std::vector<std::string> paramsToCheck = {"ctrls", "trtms", "outdir", "adpt3", "adpt5", "dbref", "features"};
+    for(auto& param : paramsToCheck) {
+        makePathAbs(params, param, configFileDir);
+    }
+}
+
 int main(int argc, char* argv[]) {
     try {
         std::string readType;
@@ -155,7 +176,6 @@ int main(int argc, char* argv[]) {
                 .add(clustering)
                 .add(output);
 
-
         // translate all positional options into subcall options
         po::positional_options_description p;
         p.add("subcall", -1);
@@ -198,6 +218,11 @@ int main(int argc, char* argv[]) {
                 notify(params);
             }
         }
+
+        // correct the paths (if they are relative)
+        fs::path configFileDir = fs::path(configFile).parent_path();
+        correctPaths(params, configFileDir);
+
         Base base(params);
 
     } catch(po::error& e) {

test/humanSE.cfg

@@ -4,7 +4,7 @@ readtype = SE # paired-end (PE) or single-end (SE)
 # absolute path of dirs containing the raw reads (additional dir for each library)
 trtms = data/human/trtms/ # treatments
 ctrls = data/human/ctrls/ # controls
-outdir = human-test-outdir # dir
+outdir = data/human-test-outdir # dir
 
 threads = 4 # number of threads
 quality = 20 # lower limit for the average quality (Phred Quality Score) of the reads
@@ -18,15 +18,15 @@ modetrm = 1 # mode of the trimming: only 5' (=0) and 3' (=1) or both (=2)
 # sequence preceeding 5'-end (N for arbitrary bp) in .fa format
 adpt5 =  
 # sequence succeeding 3'-end (N for arbitrary bp) in fa. format
-adpt3 = build/adapters3.fa
+adpt3 = ../build/adapters3.fa
 wtrim = 0 # on whether (=1) or not (=0) to include window quality trimming
 # rate of mismatches allowed when aligning adapters with read sequence 
 mmrate = 0.1 # e.g., 0.1 on a sequence length of 10 results in
 wsize = 3 # window size 
 minovlps = 10 # minimum overlaps required when merging paired-end reads
 
 ### ALIGNMENT (forwarded to segemehl.x)
-dbref = GRCh38.primary_assembly.genome_20-22.fa
+dbref = ref/GRCh38.primary_assembly.genome_20-22.fa
 accuracy = 90 # min percentage of matches per read in semi-global alignment
 minfragsco = 15 # min score of a spliced fragment 
 minfraglen = 15 # min length of a spliced fragment