Changed compile flags; build test program

CMakeLists.txt

@@ -4,6 +4,8 @@ PROJECT(gff)
 SET(PROJECT_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/include)
 SET(PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
+SET( CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -O3 -Wall -D_FILE_OFFSET_BITS=64" )
+
 SET(GFFLib_SRCS
     ${PROJECT_SOURCE_DIR}/codons.cpp
     ${PROJECT_SOURCE_DIR}/GArgs.cpp
@@ -18,6 +20,8 @@ SET(GFFLib_SRCS
 INCLUDE_DIRECTORIES(${PROJECT_INCLUDE_DIR})
 
 ADD_LIBRARY(${PROJECT_NAME} STATIC ${GFFLib_SRCS})
+ADD_EXECUTABLE(TestGFFParse ${PROJECT_SOURCE_DIR}/TestGFFParse.cpp)
+TARGET_LINK_LIBRARIES(TestGFFParse ${PROJECT_NAME})
 
 INSTALL(FILES ${CMAKE_BINARY_DIR}/lib${PROJECT_NAME}.a DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
 INSTALL(DIRECTORY ${PROJECT_INCLUDE_DIR} DESTINATION ${CMAKE_INSTALL_PREFIX})

src/TestGFFParse.cpp

@@ -1,19 +1,23 @@
 #include <iostream>
+#include <cstdio>
+#include <cstdlib>
 
 #include "gff.h"
 
-#include <cstdio>
-
 int main(int argc, char* argv[]) {
 
+    if (argc == 1 or argc > 2) {
+        std::cerr << "Usage: TestGFFParse input\n";
+        std::exit(1);
+    }
+
     GffReader reader(argv[1]);
     reader.readAll(true);
 
-
     std::cerr << "had count of " << reader.gflst.Count() << "\n";
     size_t nfeat = reader.gflst.Count();
     for (size_t i=0; i < nfeat; ++i) {
-       auto f = reader.gflst[i];
+       GffObj* f = reader.gflst[i];
        if (f->isTranscript()) {
 
            std::cout << f->getID() << '\t' << f->getGeneID() << '\t';
@@ -25,6 +29,6 @@ int main(int argc, char* argv[]) {
            std::cout << "\n";
        }
     }
-
+    std::exit(0);
 }