resolved issue when no ctrls data are provided

riasc · Jun 27, 2024 · 86bc60e · 86bc60e
1 parent 49b6cea
commit 86bc60e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,13 @@ 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).
 
+# [0.2.4]
+
+## Fix
+
+- Added lock guard for when writing progress (processed reads) to std::cout to ensure threads do not write over each other
+- Fixed bug/added check when no control data is provided
+
 # [0.2.3]
 
 ## Fix

diff --git a/src/Data.cpp b/src/Data.cpp
@@ -45,7 +45,10 @@ void Data::alignDataPrep() {
     } else {
         // make sure that data has been preprocessed (or at least selected)
         if(params["preproc"].as<std::bitset<1>>() == std::bitset<1>("1")) {
-            fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/ctrls";
+            fs::path ctrlsPath = "";
+            if(params["ctrls"].as<std::string>() != "") {
+                ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/ctrls";
+            }
             fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "preproc/trtms";
 
             /*
@@ -59,23 +62,32 @@ void Data::alignDataPrep() {
 }
 
 void Data::detectDataPrep() {
-    fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "align/ctrls";
+    fs::path ctrlsPath = "";
+    if(params["ctrls"].as<std::string>() != "") {
+        ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "align/ctrls";
+    }
     fs::path trtmsPath = fs::path(params["outdir"].as<std::string>()) / "align/trtms";
 
     GroupsPath groups = getGroupsPath(ctrlsPath, trtmsPath);
     getCondition(groups);
 }
 
 void Data::clusteringDataPrep() {
-fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
+    fs::path ctrlsPath = "";
+    if(params["ctrls"].as<std::string>() != "") {
+        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);
     getCondition(groups);
 }
 
 void Data::analysisDataPrep() {
-    fs::path ctrlsPath = fs::path(params["outdir"].as<std::string>()) / "detect/ctrls";
+    fs::path ctrlsPath = "";
+    if(params["ctrls"].as<std::string>() != "") {
+        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);
@@ -133,7 +145,7 @@ void Data::getCondition(GroupsPath& groups) {
                 exit(EXIT_FAILURE);
             }
         } else {
-            std::cout << helper::getTime() << "### ERROR - " << group.second << " has not been found in the filesystem!\n";
+            std::cout << "has not been found in the filesystem! ### ERROR### \n";
             exit(EXIT_FAILURE);
         }
     }

diff --git a/src/Preproc.cpp b/src/Preproc.cpp
@@ -17,7 +17,7 @@ Preproc::~Preproc() {}
 void Preproc::processing(fs::path& in, fs::path& out) {
     std::cout << helper::getTime() << "Trimming on sample: " << in << "\n";
 
-    std::mutex inMutex, outMutex; //
+    std::mutex inMutex, outMutex, progressMutex; //
     seqan3::sequence_file_input fin{in.string()};
     seqan3::sequence_file_output fout{out.string()};
 
@@ -28,6 +28,7 @@ void Preproc::processing(fs::path& in, fs::path& out) {
         for (auto & record : reads)
         {
             if(readcount != 0 && readcount % 100000 == 0) {
+                std::lock_guard<std::mutex> lock(progressMutex);
                 std::cout << "\r" << helper::getTime() << readcount << " reads processed " << std::flush;
             }
             readcount++;
@@ -81,7 +82,7 @@ void Preproc::processing(fs::path& inFwd, fs::path& outFwd, fs::path& inRev, fs:
     seqan3::sequence_file_output outR1unmrgSeq{outR1unmerged.string()};
     seqan3::sequence_file_output outR2unmrgSeq{outR2unmerged.string()};
 
-    std::mutex outMutex;
+    std::mutex outMutex, progressMutex;
 
     int readcount = 0;
     auto inFwdSeqBuf = inFwdSeq | seqan3::views::async_input_buffer(100);
@@ -93,6 +94,7 @@ void Preproc::processing(fs::path& inFwd, fs::path& outFwd, fs::path& inRev, fs:
             dtp::QualVector qualFwd, qualRev;
 
             if(readcount != 0 && readcount % 100000 == 0) {
+                std::lock_guard<std::mutex> lock(progressMutex);
                 std::cout << "\r" << helper::getTime() << "Processed reads: " << readcount << std::flush;
             }
             readcount++;