------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/vcflib XDG_CONFIG_HOME=/construction/biology/vcflib HOME=/construction/biology/vcflib TMPDIR="/tmp" PATH=/construction/biology/vcflib/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/vcflib XDG_CONFIG_HOME=/construction/biology/vcflib HOME=/construction/biology/vcflib TMPDIR="/tmp" PATH=/construction/biology/vcflib/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='\"1.0.0.r1.130\"' " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/vcflib/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/vcflib" EXAMPLESDIR="share/examples/vcflib" DATADIR="share/vcflib" WWWDIR="www/vcflib" ETCDIR="etc/vcflib" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/vcflib DOCSDIR=/usr/local/share/doc/vcflib EXAMPLESDIR=/usr/local/share/examples/vcflib WWWDIR=/usr/local/www/vcflib ETCDIR=/usr/local/etc/vcflib SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600102 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/fastahack-1.0.0.txz Installing /packages/All/filevercmp-g20151117.txz Installing /packages/All/fsom-g20151117_2.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.4.1.txz Installing /packages/All/mpdecimal-2.5.1.txz Installing /packages/All/ncurses-6.2.20210626.txz ===== Message from ncurses-6.2.20210626: -- { type: install message: < vcflib-1.0.0.r1.130_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> vcflib-1.0.0.r1.130_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by vcflib-1.0.0.r1.130_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> vcflib-1.0.0.r1.130_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by vcflib-1.0.0.r1.130_1 for building => SHA256 Checksum OK for ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> vcflib-1.0.0.r1.130_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by vcflib-1.0.0.r1.130_1 for building ===> Extracting for vcflib-1.0.0.r1.130_1 => SHA256 Checksum OK for ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz. Extracted Memory Use: 63.07M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for vcflib-1.0.0.r1.130_1 ===> Applying ports patches for vcflib-1.0.0.r1.130_1 from /xports/biology/vcflib/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> vcflib-1.0.0.r1.130_1 depends on executable: fastahack - found ===> vcflib-1.0.0.r1.130_1 depends on executable: filevercmp - found ===> vcflib-1.0.0.r1.130_1 depends on executable: fsom - found ===> vcflib-1.0.0.r1.130_1 depends on package: multichoose>=1.0.3 - found ===> vcflib-1.0.0.r1.130_1 depends on executable: interval_tree_test - found ===> vcflib-1.0.0.r1.130_1 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> vcflib-1.0.0.r1.130_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> vcflib-1.0.0.r1.130_1 depends on shared library: libtabix.so - found (/usr/local/lib/libtabix.so) ===> vcflib-1.0.0.r1.130_1 depends on shared library: libsw.so - found (/usr/local/lib/libsw.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> vcflib-1.0.0.r1.130_1 depends on executable: fastahack - found ===> vcflib-1.0.0.r1.130_1 depends on executable: filevercmp - found ===> vcflib-1.0.0.r1.130_1 depends on executable: fsom - found ===> vcflib-1.0.0.r1.130_1 depends on package: multichoose>=1.0.3 - found ===> vcflib-1.0.0.r1.130_1 depends on executable: interval_tree_test - found ===> vcflib-1.0.0.r1.130_1 depends on package: gmake>=4.3 - found ===> vcflib-1.0.0.r1.130_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> vcflib-1.0.0.r1.130_1 depends on shared library: libtabix.so - found (/usr/local/lib/libtabix.so) ===> vcflib-1.0.0.r1.130_1 depends on shared library: libsw.so - found (/usr/local/lib/libsw.so) ===> Configuring for vcflib-1.0.0.r1.130_1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for vcflib-1.0.0.r1.130_1 gmake[1]: Entering directory '/construction/biology/vcflib/vcflib-1.0.0-rc1-130-g7e3d806' c++ -c -o src/Variant.o src/Variant.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 c++ -c -o src/rnglib.o src/rnglib.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 c++ -c -o src/var.o src/var.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 c++ -c -o src/pdflib.o src/pdflib.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 c++ -c -o src/cdflib.o src/cdflib.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 c++ -c -o src/split.o src/split.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 c++ -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -c -o src/ssw.o src/ssw.cpp c++ -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -c -o src/ssw_cpp.o src/ssw_cpp.cpp mkdir -p bin src/Variant.cpp: In member function 'std::pair vcflib::Variant::convert_to_breakends(FastaReference&)': src/Variant.cpp:174:1: warning: control reaches end of non-void function [-Wreturn-type] }; ^ src/Variant.cpp: In member function 'bool vcflib::Variant::getInfoValueBool(std::__cxx11::string&, int)': src/Variant.cpp:502:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ src/Variant.cpp: In member function 'bool vcflib::Variant::getSampleValueBool(std::__cxx11::string&, std::__cxx11::string&, int)': src/Variant.cpp:627:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ src/Variant.cpp: In member function 'std::__cxx11::string vcflib::Variant::getSampleValueString(std::__cxx11::string&, std::__cxx11::string&, int)': src/Variant.cpp:661:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ src/Variant.cpp: In member function 'double vcflib::Variant::getSampleValueFloat(std::__cxx11::string&, std::__cxx11::string&, int)': src/Variant.cpp:699:5: warning: control reaches end of non-void function [-Wreturn-type] } ^ ar rs libvcflib.a src/Variant.o src/rnglib.o src/var.o src/pdflib.o src/cdflib.o src/split.o src/ssw.o src/ssw_cpp.o c++ -shared -Wl,-soname,libvcflib.so.1 -o libvcflib.so.1 src/Variant.o src/rnglib.o src/var.o src/pdflib.o src/cdflib.o src/split.o src/ssw.o src/ssw_cpp.o /usr/libexec/binutils234/elf/ar: creating libvcflib.a c++ src/vcfecho.cpp -o bin/vcfecho -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfnormalizesvs.cpp -o bin/vcfnormalizesvs -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/dumpContigsFromHeader.cpp -o bin/dumpContigsFromHeader -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/bFst.cpp -o bin/bFst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/pVst.cpp -o bin/pVst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/hapLrt.cpp -o bin/hapLrt -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/popStats.cpp -o bin/popStats -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/wcFst.cpp -o bin/wcFst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/iHS.cpp -o bin/iHS -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/segmentFst.cpp -o bin/segmentFst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/segmentIhs.cpp -o bin/segmentIhs -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/genotypeSummary.cpp -o bin/genotypeSummary -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/sequenceDiversity.cpp -o bin/sequenceDiversity -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/pFst.cpp -o bin/pFst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/smoother.cpp -o bin/smoother -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/LD.cpp -o bin/LD -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/plotHaps.cpp -o bin/plotHaps -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/abba-baba.cpp -o bin/abba-baba -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/permuteGPAT++.cpp -o bin/permuteGPAT++ -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/permuteSmooth.cpp -o bin/permuteSmooth -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/normalize-iHS.cpp -o bin/normalize-iHS -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/meltEHH.cpp -o bin/meltEHH -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm src/abba-baba.cpp: In function 'int sample_het(int&)': src/abba-baba.cpp:74:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ c++ src/vcfaltcount.cpp -o bin/vcfaltcount -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfhetcount.cpp -o bin/vcfhetcount -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfhethomratio.cpp -o bin/vcfhethomratio -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcffilter.cpp -o bin/vcffilter -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcf2tsv.cpp -o bin/vcf2tsv -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgenotypes.cpp -o bin/vcfgenotypes -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfannotategenotypes.cpp -o bin/vcfannotategenotypes -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcommonsamples.cpp -o bin/vcfcommonsamples -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfremovesamples.cpp -o bin/vcfremovesamples -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfkeepsamples.cpp -o bin/vcfkeepsamples -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfsamplenames.cpp -o bin/vcfsamplenames -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgenotypecompare.cpp -o bin/vcfgenotypecompare -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcffixup.cpp -o bin/vcffixup -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfclassify.cpp -o bin/vcfclassify -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfsamplediff.cpp -o bin/vcfsamplediff -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfremoveaberrantgenotypes.cpp -o bin/vcfremoveaberrantgenotypes -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfrandom.cpp -o bin/vcfrandom -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfparsealts.cpp -o bin/vcfparsealts -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfstats.cpp -o bin/vcfstats -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfflatten.cpp -o bin/vcfflatten -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfprimers.cpp -o bin/vcfprimers -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfnumalt.cpp -o bin/vcfnumalt -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcleancomplex.cpp -o bin/vcfcleancomplex -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfintersect.cpp -o bin/vcfintersect -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfannotate.cpp -o bin/vcfannotate -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfallelicprimitives.cpp -o bin/vcfallelicprimitives -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfoverlay.cpp -o bin/vcfoverlay -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfaddinfo.cpp -o bin/vcfaddinfo -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfkeepinfo.cpp -o bin/vcfkeepinfo -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfkeepgeno.cpp -o bin/vcfkeepgeno -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfafpath.cpp -o bin/vcfafpath -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcountalleles.cpp -o bin/vcfcountalleles -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcflength.cpp -o bin/vcflength -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfdistance.cpp -o bin/vcfdistance -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfrandomsample.cpp -o bin/vcfrandomsample -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfentropy.cpp -o bin/vcfentropy -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfglxgt.cpp -o bin/vcfglxgt -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfroc.cpp -o bin/vcfroc -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcheck.cpp -o bin/vcfcheck -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfstreamsort.cpp -o bin/vcfstreamsort -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfuniq.cpp -o bin/vcfuniq -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfuniqalleles.cpp -o bin/vcfuniqalleles -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfremap.cpp -o bin/vcfremap -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcf2fasta.cpp -o bin/vcf2fasta -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfsitesummarize.cpp -o bin/vcfsitesummarize -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfbreakmulti.cpp -o bin/vcfbreakmulti -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcreatemulti.cpp -o bin/vcfcreatemulti -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfevenregions.cpp -o bin/vcfevenregions -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcat.cpp -o bin/vcfcat -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgenosummarize.cpp -o bin/vcfgenosummarize -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgenosamplenames.cpp -o bin/vcfgenosamplenames -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgeno2haplo.cpp -o bin/vcfgeno2haplo -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfleftalign.cpp -o bin/vcfleftalign -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcombine.cpp -o bin/vcfcombine -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgeno2alleles.cpp -o bin/vcfgeno2alleles -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfindex.cpp -o bin/vcfindex -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcf2dag.cpp -o bin/vcf2dag -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfsample2info.cpp -o bin/vcfsample2info -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfqual2info.cpp -o bin/vcfqual2info -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfinfo2qual.cpp -o bin/vcfinfo2qual -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfglbound.cpp -o bin/vcfglbound -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfunphase.cpp -o bin/vcfunphase -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfnull2ref.cpp -o bin/vcfnull2ref -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfinfosummarize.cpp -o bin/vcfinfosummarize -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm gmake[1]: Leaving directory '/construction/biology/vcflib/vcflib-1.0.0-rc1-130-g7e3d806' SUCCEEDED 00:01:01 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> vcflib-1.0.0.r1.130_1 depends on executable: fastahack - found ===> vcflib-1.0.0.r1.130_1 depends on executable: filevercmp - found ===> vcflib-1.0.0.r1.130_1 depends on executable: fsom - found ===> vcflib-1.0.0.r1.130_1 depends on package: multichoose>=1.0.3 - found ===> vcflib-1.0.0.r1.130_1 depends on executable: interval_tree_test - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for vcflib-1.0.0.r1.130_1 ===> vcflib-1.0.0.r1.130_1 depends on executable: fastahack - found ===> vcflib-1.0.0.r1.130_1 depends on executable: filevercmp - found ===> vcflib-1.0.0.r1.130_1 depends on executable: fsom - found ===> vcflib-1.0.0.r1.130_1 depends on package: multichoose>=1.0.3 - found ===> vcflib-1.0.0.r1.130_1 depends on executable: interval_tree_test - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/vcflib/vcflib-1.0.0-rc1-130-g7e3d806' mkdir -p bin c++ src/vcfecho.cpp -o bin/vcfecho -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfnormalizesvs.cpp -o bin/vcfnormalizesvs -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/dumpContigsFromHeader.cpp -o bin/dumpContigsFromHeader -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/bFst.cpp -o bin/bFst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/pVst.cpp -o bin/pVst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/hapLrt.cpp -o bin/hapLrt -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/popStats.cpp -o bin/popStats -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/wcFst.cpp -o bin/wcFst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/iHS.cpp -o bin/iHS -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/segmentFst.cpp -o bin/segmentFst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/segmentIhs.cpp -o bin/segmentIhs -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/genotypeSummary.cpp -o bin/genotypeSummary -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/sequenceDiversity.cpp -o bin/sequenceDiversity -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/pFst.cpp -o bin/pFst -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/smoother.cpp -o bin/smoother -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/LD.cpp -o bin/LD -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/plotHaps.cpp -o bin/plotHaps -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/abba-baba.cpp -o bin/abba-baba -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm src/abba-baba.cpp: In function 'int sample_het(int&)': src/abba-baba.cpp:74:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ c++ src/permuteGPAT++.cpp -o bin/permuteGPAT++ -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/permuteSmooth.cpp -o bin/permuteSmooth -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/normalize-iHS.cpp -o bin/normalize-iHS -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/meltEHH.cpp -o bin/meltEHH -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfaltcount.cpp -o bin/vcfaltcount -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfhetcount.cpp -o bin/vcfhetcount -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfhethomratio.cpp -o bin/vcfhethomratio -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcffilter.cpp -o bin/vcffilter -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcf2tsv.cpp -o bin/vcf2tsv -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgenotypes.cpp -o bin/vcfgenotypes -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfannotategenotypes.cpp -o bin/vcfannotategenotypes -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcommonsamples.cpp -o bin/vcfcommonsamples -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfremovesamples.cpp -o bin/vcfremovesamples -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfkeepsamples.cpp -o bin/vcfkeepsamples -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfsamplenames.cpp -o bin/vcfsamplenames -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgenotypecompare.cpp -o bin/vcfgenotypecompare -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcffixup.cpp -o bin/vcffixup -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfclassify.cpp -o bin/vcfclassify -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfsamplediff.cpp -o bin/vcfsamplediff -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfremoveaberrantgenotypes.cpp -o bin/vcfremoveaberrantgenotypes -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfrandom.cpp -o bin/vcfrandom -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfparsealts.cpp -o bin/vcfparsealts -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfstats.cpp -o bin/vcfstats -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfflatten.cpp -o bin/vcfflatten -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfprimers.cpp -o bin/vcfprimers -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfnumalt.cpp -o bin/vcfnumalt -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcleancomplex.cpp -o bin/vcfcleancomplex -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfintersect.cpp -o bin/vcfintersect -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfannotate.cpp -o bin/vcfannotate -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfallelicprimitives.cpp -o bin/vcfallelicprimitives -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfoverlay.cpp -o bin/vcfoverlay -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfaddinfo.cpp -o bin/vcfaddinfo -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfkeepinfo.cpp -o bin/vcfkeepinfo -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfkeepgeno.cpp -o bin/vcfkeepgeno -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfafpath.cpp -o bin/vcfafpath -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcountalleles.cpp -o bin/vcfcountalleles -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcflength.cpp -o bin/vcflength -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfdistance.cpp -o bin/vcfdistance -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfrandomsample.cpp -o bin/vcfrandomsample -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfentropy.cpp -o bin/vcfentropy -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfglxgt.cpp -o bin/vcfglxgt -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfroc.cpp -o bin/vcfroc -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcheck.cpp -o bin/vcfcheck -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfstreamsort.cpp -o bin/vcfstreamsort -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfuniq.cpp -o bin/vcfuniq -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfuniqalleles.cpp -o bin/vcfuniqalleles -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfremap.cpp -o bin/vcfremap -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcf2fasta.cpp -o bin/vcf2fasta -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfsitesummarize.cpp -o bin/vcfsitesummarize -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfbreakmulti.cpp -o bin/vcfbreakmulti -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcreatemulti.cpp -o bin/vcfcreatemulti -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfevenregions.cpp -o bin/vcfevenregions -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcat.cpp -o bin/vcfcat -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgenosummarize.cpp -o bin/vcfgenosummarize -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgenosamplenames.cpp -o bin/vcfgenosamplenames -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgeno2haplo.cpp -o bin/vcfgeno2haplo -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfleftalign.cpp -o bin/vcfleftalign -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfcombine.cpp -o bin/vcfcombine -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfgeno2alleles.cpp -o bin/vcfgeno2alleles -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfindex.cpp -o bin/vcfindex -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcf2dag.cpp -o bin/vcf2dag -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfsample2info.cpp -o bin/vcfsample2info -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfqual2info.cpp -o bin/vcfqual2info -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfinfo2qual.cpp -o bin/vcfinfo2qual -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfglbound.cpp -o bin/vcfglbound -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfunphase.cpp -o bin/vcfunphase -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfnull2ref.cpp -o bin/vcfnull2ref -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm c++ src/vcfinfosummarize.cpp -o bin/vcfinfosummarize -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -pipe -O2 -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -pipe -O2 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -L. -lvcflib -L/usr/local/lib -lsw -ltabix -lhts -lfastahack -lfilevercmp -lpthread -lz -lm mkdir -p /construction/biology/vcflib/stage/usr/local/bin mkdir -p /construction/biology/vcflib/stage/usr/local/include/vcflib mkdir -p /construction/biology/vcflib/stage/usr/local/lib install -c bin/* /construction/biology/vcflib/stage/usr/local/bin install -c src/*.h src/*.hpp /construction/biology/vcflib/stage/usr/local/include/vcflib install -c libvcflib.a libvcflib.so.1 /construction/biology/vcflib/stage/usr/local/lib strip /construction/biology/vcflib/stage/usr/local/bin/* /construction/biology/vcflib/stage/usr/local/lib/libvcflib.so.1 gmake[1]: Leaving directory '/construction/biology/vcflib/vcflib-1.0.0-rc1-130-g7e3d806' install -l rs /construction/biology/vcflib/stage/usr/local/lib/libvcflib.so.1 /construction/biology/vcflib/stage/usr/local/lib/libvcflib.so ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:05:54 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for vcflib-1.0.0.r1.130_1 file sizes/checksums [104]: 0% file sizes/checksums [104]: 96% file sizes/checksums [104]: 100% packing files [104]: 0% packing files [104]: 96% packing files [104]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:20 TOTAL TIME 00:07:29