-------------------------------------------------------------------------------
-- 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-2.2.8.txz
Installing /packages/All/ncurses-6.2.20200831.txz
Installing /packages/All/readline-8.0.4.txz
Installing /packages/All/gettext-runtime-0.21.txz
Installing /packages/All/openssl-1.1.1g,1.txz
Installing /packages/All/python37-3.7.9.txz
=====
Message from python37-3.7.9:

--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

py37-gdbm       databases/py-gdbm@py37
py37-sqlite3    databases/py-sqlite3@py37
py37-tkinter    x11-toolkits/py-tkinter@py37
Installing /packages/All/multichoose-1.0.3.2.txz
Installing /packages/All/intervaltree-g20151213_2.txz
Installing /packages/All/gmake-4.3_2.txz
Installing /packages/All/libdeflate-1.6.txz
Installing /packages/All/libnghttp2-1.41.0.txz
Installing /packages/All/ca_root_nss-3.56.txz
=====
Message from ca_root_nss-3.56:

--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.

Assessment and verification of trust is the complete responsibility of the
system administrator.


This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.

This enables SSL Certificate Verification by client software without manual
intervention.

If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.

  * /etc/ssl/cert.pem
  * /usr/local/etc/ssl/cert.pem
  * /usr/local/openssl/cert.pem
Installing /packages/All/curl-7.72.0.txz
Installing /packages/All/htslib-1.10.2.txz
Installing /packages/All/tabixpp-1.0.0.10_1.txz
Installing /packages/All/smithwaterman-g20160702.txz

SUCCEEDED 00:00:15

-------------------------------------------------------------------------------
-- Phase: check-sanity
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: pkg-depends
-------------------------------------------------------------------------------

===>   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 00:00:01

-------------------------------------------------------------------------------
-- 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 00:00:01

-------------------------------------------------------------------------------
-- 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, vcflib::Variant> 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/binutils227/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
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/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
gmake[1]: Leaving directory '/construction/biology/vcflib/vcflib-1.0.0-rc1-130-g7e3d806'

SUCCEEDED 00:02:09

-------------------------------------------------------------------------------
-- 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'
/bin/sh /xports/Mk/Scripts/relative_link.sh /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 00:11:41

-------------------------------------------------------------------------------
-- 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 00:00:00

-------------------------------------------------------------------------------
-- 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 00:00:39
TOTAL TIME 00:14:50