Save the number of reads and the average read length per library in a…

… metadata file

src/brownie.cpp

@@ -145,6 +145,10 @@ void Brownie::stageOne()
         cout << "done (" << Util::stopChronoStr() << ")" << endl;
 
         delete readParser;
+
+        // write metadata for all libraries
+        libraries.writeMetadata(settings.getTempDirectory());
+
         cout << "Stage 1 finished.\n" << endl;
 }
 

src/library.cpp

@@ -71,6 +71,27 @@ std::ostream &operator<<(std::ostream &out, const FileType &fileType) {
         return out;
 }
 
+void ReadLibrary::readMetadata(const string& path)
+{
+        ifstream ifs((path + inputFilename + ".met").c_str());
+        if (!ifs.good())
+                return;
+        string line, tmp;
+        getline(ifs, line);
+        stringstream(line) >> tmp >> tmp >> tmp >> numReads;
+        getline(ifs, line);
+        stringstream(line) >> tmp >> tmp >> tmp >> avgReadLength;
+        ifs.close();
+}
+
+void ReadLibrary::writeMetadata(const string& path) const
+{
+        ofstream ofs((path + inputFilename + ".met").c_str());
+        ofs << "Number of reads: " << numReads << "\n"
+            << "Average read length: " << avgReadLength << endl;
+        ofs.close();
+}
+
 // ============================================================================
 // READLIBRARY CLASS
 // ============================================================================
@@ -584,3 +605,15 @@ void LibraryContainer::joinIOThreads()
         workBlocks.clear();             // contains only a termination msg
         outputBlocks.clear();           // contains only a termination msg
 }
+
+void LibraryContainer::readMetadata(const string& path)
+{
+        for (auto& it : container)
+                it.readMetadata(path);
+}
+
+void LibraryContainer::writeMetadata(const string& path) const
+{
+        for (const auto& it : container)
+                it.writeMetadata(path);
+}

src/library.h

@@ -127,6 +127,18 @@ class ReadLibrary
         double getAvgReadLength() const {
                 return avgReadLength;
         }
+
+        /**
+         * Read the metadata to disk
+         * @param path Path to dir where the metadata should be read
+         */
+        void readMetadata(const std::string& path);
+
+        /**
+         * Write the metadata to disk
+         * @param path Path to dir where the metadata should be written
+         */
+        void writeMetadata(const std::string& path) const;
 };
 
 // ============================================================================
@@ -387,6 +399,18 @@ class LibraryContainer
          * routine is called will result in undefined behavior
          */
         void joinIOThreads();
+
+        /**
+         * Read the metadata to disk
+         * @param path Path to dir where the metadata should be read
+         */
+        void readMetadata(const std::string& path);
+
+        /**
+         * Write the metadata to disk
+         * @param path Path to dir where the metadata should be written
+         */
+        void writeMetadata(const std::string& path) const;
 };
 
 #endif

src/settings.cpp

@@ -215,4 +215,7 @@ void Settings::parseCommandLineArguments(int argc, char** args,
         ofs << args[argc-1] << endl;
 
         ofs.close();
+
+        // try to read the metadata for each library
+        libCont.readMetadata(getTempDirectory());
 }