/usr/bin/c++    -Wall -Wextra -Werror -fPIC -fsigned-char -Wno-deprecated-declarations -msse3 -O3 -g  -std=c++11 -Wno-unused-parameter -Wno-unused-variable -Wno-unused-function -Wno-error=unused-but-set-variable -Wno-error=unused-but-set-parameter    CMakeFiles/bamrealignment.dir/realignment/bamrealignment.cpp.o CMakeFiles/bamrealignment.dir/realignment/Realigner.cpp.o CMakeFiles/bamrealignment.dir/Util/Utils.cpp.o CMakeFiles/bamrealignment.dir/Util/OptArgs.cpp.o CMakeFiles/bamrealignment.dir/IonVersion.cpp.o  -o bamrealignment -rdynamic ../bamtools-2.4.0.20150702+git15eadb925f-install/lib/bamtools/libbamtools.a -lz -lpthread