minor

.gitignore

@@ -1,14 +1,4 @@
 .vscode/*
 build
 cryfa
-keygen
-
-origin
-*.fa
-*.fq
-in
-fa
-fq
-mori
-origfa
-origfq
+keygen

CMakeLists.txt

@@ -1,18 +1,42 @@
 cmake_minimum_required(VERSION 3.3.2)
+
 project(cryfa)
 
-SET(CMAKE_BUILD_TYPE Release)
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -pthread -O3")
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Release)
+endif()
 
-file(GLOB CRYPTOPP_SOURCE "src/cryptopp/*.cpp")
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED 11)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3")
+set(CMAKE_CXX_FLAGS_DEBUG "-g")
 
-add_executable(cryfa
+include_directories(${CMAKE_SOURCE_DIR}/src/include)
+
+find_package(Threads REQUIRED)
+
+file(GLOB CRYPTOPP_SOURCE "src/cryptopp/*.cpp")
+add_library(libCryptopp OBJECT 
     ${CRYPTOPP_SOURCE}
-    src/cryfa.cpp
+)
+
+add_library(libCryfaCommon OBJECT
     src/endecrypto.cpp
     src/fasta.cpp
     src/fastq.cpp
-    src/security.cpp)
+    src/security.cpp
+)
+
+add_executable(cryfa
+    src/cryfa.cpp
+)
+
+target_link_libraries(cryfa
+    Threads::Threads
+    libCryfaCommon
+    libCryptopp
+)
 
 add_executable(keygen
-    src/keygen.cpp)
+    src/keygen.cpp
+)

install.sh

@@ -2,7 +2,7 @@
 
 if [ ! -d build ]; then mkdir -p build; fi
 cd build
-# rm CMakeCache.txt
+rm CMakeCache.txt
 cmake ..
 make -j4
 mv cryfa ..

src/application.hpp

@@ -52,7 +52,6 @@ class application {
 
  public:
   application() = default;
-
   void exe(int, char**);
 };
 
@@ -83,11 +82,9 @@ void application::exe_decrypt_decompress() {
   std::ifstream in(DEC_FNAME);
   switch (in.peek()) {
     case (char)127:
-      // std::cerr << "Decompressing...\n";
       fa.decompress();
       break;
     case (char)126:
-      // std::cerr << "Decompressing...\n";
       fq.decompress();
       break;
     case (char)125:

src/def.hpp

@@ -62,11 +62,6 @@ struct POWER<B, 0> {
   LOOP(i, S) LOOP(j, S) LOOP6(k, l, m, n, o, p, S)
 #define IGNORE_THIS_LINE(in) \
   (in).ignore(std::numeric_limits<std::streamsize>::max(), '\n')
-#define REWIND(in)                \
-  {                               \
-    (in).clear();                 \
-    (in).seekg(0, std::ios::beg); \
-  }
 
 // Constants
 static const std::string THR_ID_HDR = "THRD=";  /**< @brief Thread ID header */
@@ -81,7 +76,7 @@ static const std::string UPK_FNAME =
 static const std::string USH_FNAME =
     "CRYFA_USH";                     /**< @brief Unshuffled file name*/
 constexpr byte DEF_N_THR = 8;        /**< @brief Default number of threads */
-constexpr u64 BLOCK_SIZE = 8 * 1024; /**< @brief To read from input file*/
+constexpr u64 BLOCK_SIZE = 8 * 1024; /**< @brief To read/write from/to file */
 constexpr byte C1 = 2;               /**< @brief       Cat 1  =  2 */
 constexpr byte C2 = 3;               /**< @brief       Cat 2  =  3 */
 constexpr byte MIN_C3 = 4;           /**< @brief  4 <= Cat 3 <=  6 */

src/endecrypto.cpp

@@ -1018,7 +1018,6 @@ void EnDecrypto::unshuffle_block(byte threadID) {
 
     // Write header containing threadID for each partially unshuffled file
     ushfile << THR_ID_HDR + std::to_string(threadID) << '\n';
-
     ushfile << unshText << '\n';
 
     // Ignore to go to the next related chunk
@@ -1042,23 +1041,26 @@ void EnDecrypto::join_packed_files(const std::string& headers,
   byte t;  // For threads
   std::ifstream pkFile[n_threads];
   std::ofstream pckdFile(PCKD_FNAME);  // Packed file
+  std::string content;
+  content.reserve(BLOCK_SIZE);
+  auto write_content = [&]() { pckdFile << content; };
 
   switch (fT) {
     case 'A':
-      pckdFile << (char)127;
+      content += (char)127;
       break;  // Fasta
     case 'Q':
-      pckdFile << (char)126;
+      content += (char)126;
       break;  // Fastq
     default:
       break;
   }
-  pckdFile << (!stop_shuffle ? (char)128 : (char)129);
-  pckdFile << headers;
-  pckdFile << (char)254;  // To detect headers in decryptor
+  content += (!stop_shuffle ? (char)128 : (char)129);
+  content += headers;
+  content += (char)254;  // To detect headers in decryptor
   if (fT == 'Q') {
-    pckdFile << qscores;
-    pckdFile << (justPlus ? (char)253 : '\n');
+    content += qscores;
+    content += (justPlus ? (char)253 : '\n');
   }
 
   // Input files
@@ -1072,14 +1074,21 @@ void EnDecrypto::join_packed_files(const std::string& headers,
 
       while (std::getline(pkFile[t], line).good() &&
              line != THR_ID_HDR + std::to_string(t)) {
-        if (prevLineNotThrID) pckdFile << '\n';
-        pckdFile << line;
+        if (prevLineNotThrID) content += '\n';
+        content += line;
+
+        if (content.size() >= BLOCK_SIZE) {
+          write_content();
+          content.clear();
+          content.reserve(BLOCK_SIZE);
+        }
 
         prevLineNotThrID = true;
       }
     }
   }
-  pckdFile << (char)252;
+  content += (char)252;
+  write_content();
 
   // Close/delete input/output files
   pckdFile.close();
@@ -1098,6 +1107,9 @@ void EnDecrypto::join_unpacked_files() const {
   byte t;  // For threads
   std::ifstream upkdFile[n_threads];
   for (t = n_threads; t--;) upkdFile[t].open(UPK_FNAME + std::to_string(t));
+  std::string content;
+  content.reserve(BLOCK_SIZE);
+  auto write_content = [&]() { std::cout << content; };
 
   bool prevLineNotThrID;  // If previous line was "THRD=" or not
   while (!upkdFile[0].eof()) {
@@ -1106,15 +1118,22 @@ void EnDecrypto::join_unpacked_files() const {
 
       for (std::string line; std::getline(upkdFile[t], line).good() &&
                              line != THR_ID_HDR + std::to_string(t);) {
-        if (prevLineNotThrID) std::cout << '\n';
-        std::cout << line;
+        if (prevLineNotThrID) content += '\n';
+        content += line;
+
+        if (content.size() >= BLOCK_SIZE) {
+          write_content();
+          content.clear();
+          content.reserve(BLOCK_SIZE);
+        }
 
         prevLineNotThrID = true;
       }
 
-      if (prevLineNotThrID) std::cout << '\n';
+      if (prevLineNotThrID) content += '\n';
     }
   }
+  write_content();
 
   // Close/delete input/output files
   for (t = n_threads; t--;) {
@@ -1131,9 +1150,12 @@ void EnDecrypto::join_unpacked_files() const {
 void EnDecrypto::join_shuffled_files() const {
   std::ifstream shFile[n_threads];
   std::ofstream shdFile(PCKD_FNAME);  // Output Shuffled file
+  std::string content;
+  content.reserve(BLOCK_SIZE);
+  auto write_content = [&]() { shdFile << content; };
 
-  shdFile << (char)125;
-  shdFile << (!stop_shuffle ? (char)128 : (char)129);
+  content += (char)125;
+  content += (!stop_shuffle ? (char)128 : (char)129);
 
   // Input files
   for (byte t = n_threads; t--;) shFile[t].open(SH_FNAME + std::to_string(t));
@@ -1144,13 +1166,20 @@ void EnDecrypto::join_shuffled_files() const {
 
       for (std::string line; std::getline(shFile[t], line).good() &&
                              line != THR_ID_HDR + std::to_string(t);) {
-        if (prevLineNotThrID) shdFile << '\n';
-        shdFile << line;
+        if (prevLineNotThrID) content += '\n';
+        content += line;
+
+        if (content.size() >= BLOCK_SIZE) {
+          write_content();
+          content.clear();
+          content.reserve(BLOCK_SIZE);
+        }
 
         prevLineNotThrID = true;
       }
     }
   }
+  write_content();
 
   // Close/delete input/output files
   shdFile.close();
@@ -1169,20 +1198,30 @@ void EnDecrypto::join_unshuffled_files() const {
   byte t;  // For threads
   std::ifstream ushdFile[n_threads];
   for (t = n_threads; t--;) ushdFile[t].open(USH_FNAME + std::to_string(t));
+  std::string content;
+  content.reserve(BLOCK_SIZE);
+  auto write_content = [&]() { std::cout << content; };
 
   while (!ushdFile[0].eof()) {
     for (t = 0; t != n_threads; ++t) {
       bool prevLineNotThrID = false;  // If previous line was "THR=" or not
 
       for (std::string line; std::getline(ushdFile[t], line).good() &&
                              line != THR_ID_HDR + std::to_string(t);) {
-        if (prevLineNotThrID) std::cout << '\n';
-        std::cout << line;
+        if (prevLineNotThrID) content += '\n';
+        content += line;
+
+        if (content.size() >= BLOCK_SIZE) {
+          write_content();
+          content.clear();
+          content.reserve(BLOCK_SIZE);
+        }
 
         prevLineNotThrID = true;
       }
     }
   }
+  write_content();
 
   // Close/delete input/output files
   for (t = n_threads; t--;) {