[COMPAT] Build compatibility

 - CMakeLists.txt is case sensitive in earlier cmake versions
 - Make sure no copy construction of std::ofstream is attempted
 - Suppress warnings in gcc

Author: Leon Kuchenbecker

src/CMakeLists.txt

@@ -16,6 +16,7 @@ if(GIT_FOUND)
         COMMAND ${GIT_EXECUTABLE} describe --dirty=-dirty
         WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
         OUTPUT_VARIABLE DESCRIBE_BUILD
+	ERROR_QUIET
         OUTPUT_STRIP_TRAILING_WHITESPACE)
     #    string(REGEX MATCH "[0-9]+" BUILD_NUMBER ${DESCRIBE_BUILD})
 endif()
@@ -89,7 +90,7 @@ add_executable (imseq
 target_link_libraries (imseq ${SEQAN_LIBRARIES})
 
 # Add CXX flags found by find_package (SeqAn).
-set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")
+set (CMAKE_CXX_FLAGS "-Wno-address ${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")
 
 # ----------------------------------------------------------------------------
 # Installation

src/imseq.h

@@ -1217,10 +1217,10 @@ CharString getBcOutPath(CdrOptions const & options, AminoAcid)
     return options.aminoOutBc;
 }
 
-inline std::ofstream openAndCheck(CharString const & path)
+inline std::ofstream * openAndCheck(CharString const & path)
 {
-    std::ofstream ofs(toCString(path));
-    if (!ofs.good())
+    std::ofstream * ofs = new std::ofstream(toCString(path));
+    if (!ofs->good())
     {
         std::cerr << "\n[ERROR] Cannot open output file '" << path << "'!" << std::endl;
         std::exit(1);
@@ -1273,17 +1273,21 @@ void _writeClonotypeCounts(std::map<Clone<TAlphabet>, ClusterResult>const & clon
     // ============================================================================
     if (outPath != "")
     {
-        std::ofstream ofs = openAndCheck(outPath);
+        std::ofstream * ofsPtr = openAndCheck(outPath);
+        std::ofstream & ofs = *ofsPtr;
         for (typename TCounter::const_iterator fpCount = fingerPrintCounter.begin(); fpCount!=fingerPrintCounter.end(); ++fpCount)
             ofs << fpCount->first << '\t' << fpCount->second.count << std::endl;
         ofs.close();
+        delete ofsPtr;
     }
     if (bcOutPath != "")
     {
-        std::ofstream ofs = openAndCheck(bcOutPath);
+        std::ofstream * ofsPtr = openAndCheck(bcOutPath);
+        std::ofstream & ofs = *ofsPtr;
         for (typename TCounter::const_iterator fpCount = fingerPrintCounter.begin(); fpCount!=fingerPrintCounter.end(); ++fpCount)
             ofs << fpCount->first << '\t' << fpCount->second.contribBCs.size() << std::endl;
         ofs.close();
+        delete ofsPtr;
     }
 
 }

unit_test/CmakeLists.txt unit_test/CMakeLists.txtunit_test/CmakeLists.txt renamed to unit_test/CMakeLists.txt

@@ -25,7 +25,7 @@ To build IMSEQ, you will need
 Invoke the following commands to build IMSEQ:
 
 $ cmake ./seqan_minimal/
-$ make
+$ make imseq
 
 If you do not want to use your systems default C++ compiler, you can specify
 the path to your C++ compiler as shown in this example: