fix selection of control data

Author: riasc

CHANGELOG.md

@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+# [0.2.5]
+
+# Fix
+- Fixed a variable shadowing issue in path handling that prevented the control path from being properly set. The inner declaration of ctrlsPath inside the 
+conditional block was creating a local variable instead of modifying the outer one, causing the control path to remain empty regardless of input parameters.
+
 # [0.2.4]
 
 # Fix

README.md

@@ -1,6 +1,6 @@
 [![docker-release](https://github.com/Ibvt/RNAnue/actions/workflows/docker.yml/badge.svg)](https://github.com/Ibvt/RNAnue/actions/workflows/docker.yml)
 
-# RNAnue - 0.2.4
+# RNAnue - 0.2.5
 
 ## About
 RNAnue is a comprehensive analysis to detect RNA-RNA interactions from Direct-Duplex-Detection (DDD) data.

src/Data.cpp

@@ -48,7 +48,7 @@ void Data::alignDataPrep() {
         if(params["preproc"].as<std::bitset<1>>() == std::bitset<1>("1")) {
             fs::path ctrlsPath = "";
             if(params["ctrls"].as<std::string>() != "") {
-                fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/ctrls";
+                ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/ctrls";
             }
             fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/trtms";
 
@@ -65,7 +65,7 @@ void Data::alignDataPrep() {
 void Data::detectDataPrep() {
     fs::path ctrlsPath = "";
     if(params["ctrls"].as<std::string>() != "") {
-        fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "align/ctrls";
+        ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "align/ctrls";
     }
     fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "align/trtms";
 
@@ -76,7 +76,7 @@ void Data::detectDataPrep() {
 void Data::clusteringDataPrep() {
     fs::path ctrlsPath = "";
     if(params["ctrls"].as<std::string>() != "") {
-        fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
+        ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
     }
     fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "detect/trtms";
 
@@ -87,7 +87,7 @@ void Data::clusteringDataPrep() {
 void Data::analysisDataPrep() {
     fs::path ctrlsPath = "";
     if(params["ctrls"].as<std::string>() != "") {
-        fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
+        ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
     }
     fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "detect/trtms";