biology/vcflib: Update to 1.0.2

Switch to github submodules for most deps rather than patch build system
Fixes build on powerpc64 and aarch64, possibly others

Changes:        https://github.com/vcflib/vcflib/tags

PR:             259622
Reported by:    pkubaj

7 files changed, 160 insertions, 395 deletions

diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile
index ce0cdd503e41..87cf159dd0ba 100644
--- a/biology/vcflib/Makefile
+++ b/biology/vcflib/Makefile
@@ -1,8 +1,6 @@
 PORTNAME=		vcflib
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.0.0-rc1-130
-PORTREVISION=	1
-DISTVERSIONSUFFIX=	-g7e3d806
+DISTVERSION=		1.0.2
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -10,47 +8,26 @@ COMMENT=	C++ library and CLI tools for parsing and manipulating VCF files
 
 LICENSE=	MIT
 
-BROKEN_aarch64=		fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
+# Should be rechecked since upgrade to 1.0.2.  Same error resolved on aarch64.
 BROKEN_riscv64=		fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
 
 LIB_DEPENDS=	libhts.so:biology/htslib \
-		libtabix.so:biology/tabixpp \
-		libsw.so:biology/smithwaterman
-COMMON_DEPENDS=	fastahack:biology/fastahack \
-		filevercmp:sysutils/filevercmp \
-		fsom:science/fsom \
-		multichoose>=1.0.3:math/multichoose \
-		interval_tree_test:math/intervaltree
-BUILD_DEPENDS=	${COMMON_DEPENDS}
-RUN_DEPENDS=	${COMMON_DEPENDS}
+		libtabix.so:biology/tabixpp
 
-USES=		gmake shebangfix
-USE_LDCONFIG=	yes
+USES=		cmake localbase:ldflags pkgconfig shebangfix
 USE_GITHUB=	yes
 GH_ACCOUNT=	ekg
-
-CXXFLAGS+=	-I${LOCALBASE}/include/smithwaterman \
-		-I${LOCALBASE}/include/multichoose \
-		-I${LOCALBASE}/include/filevercmp \
-		-I${LOCALBASE}/include/fastahack \
-		-I${LOCALBASE}/include/intervaltree \
-		-DVERSION='\"${PORTVERSION}\"'
+GH_TUPLE=	ekg:smithwaterman:2610e25:smithwaterman/smithwaterman \
+		ekg:multichoose:68733cd:multichoose/multichoose \
+		ekg:fastahack:bb33265:fastahack/fastahack \
+		ekg:intervaltree:17ddd57:intervaltree/intervaltree \
+		ekg:fsom:a6ef318:fsom/fsom \
+		ekg:filevercmp:1a9b779:filevercmp/filevercmp \
+		google:googletest:d225acc:googletest/googletest \
+		edawson:libVCFH:615a06b:libVCFH/libVCFH \
+		simd-everywhere:simde-no-tests:2931676:simd/src/simde
 
 # Clang and GCC disable sse2 by default on i386, but it's required for vcflib
 CFLAGS_i386=	-msse2
 
-MAKEFILE=	${FILESDIR}/Makefile.external-libs
-INSTALL_TARGET=	install-strip
-
-.include <bsd.port.options.mk>
-
-.if ${ARCH} == powerpc64le
-CFLAGS+=	-DNO_WARN_X86_INTRINSICS
-USES+=		compiler:gcc-c++11-lib 
-.endif
-
-post-install:
-	${RLN} ${STAGEDIR}${PREFIX}/lib/libvcflib.so.1 \
-		${STAGEDIR}${PREFIX}/lib/libvcflib.so
-
 .include <bsd.port.mk>
diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo
index 985916a8d85b..6483bb55115d 100644
--- a/biology/vcflib/distinfo
+++ b/biology/vcflib/distinfo
@@ -1,3 +1,21 @@
-TIMESTAMP = 1523243322
-SHA256 (ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz) = 8ec24354dfc7a87c011c865ab75f3eb72646768ab9cb6eff4263e69763338478
-SIZE (ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz) = 20138644
+TIMESTAMP = 1635902784
+SHA256 (ekg-vcflib-v1.0.2_GH0.tar.gz) = a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910
+SIZE (ekg-vcflib-v1.0.2_GH0.tar.gz) = 19215813
+SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce
+SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160
+SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297
+SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558
+SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
+SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
+SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1
+SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488
+SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b
+SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686
+SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
+SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053
+SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa
+SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815
+SHA256 (edawson-libVCFH-615a06b_GH0.tar.gz) = 2774c26c55e1d155fe803b492a745a1d2a3659f4fdbe248d3187ce03edf87223
+SIZE (edawson-libVCFH-615a06b_GH0.tar.gz) = 2295
+SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63
+SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996
diff --git a/biology/vcflib/files/Makefile.external-libs b/biology/vcflib/files/Makefile.external-libs
deleted file mode 100644
index ae030a517b44..000000000000
--- a/biology/vcflib/files/Makefile.external-libs
+++ /dev/null
@@ -1,207 +0,0 @@
-#OBJ_DIR = ./
-HEADERS = src/Variant.h \
-		  src/split.h \
-		  src/pdflib.hpp \
-		  src/var.hpp \
-                  src/cdflib.hpp \
-		  src/rnglib.hpp \
-		  src/join.h
-SOURCES = src/Variant.cpp \
-		  src/rnglib.cpp \
-		  src/var.cpp \
-		  src/pdflib.cpp \
-		  src/cdflib.cpp \
-		  src/split.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-
-VCF_LIB_LOCAL:=$(shell pwd)
-BIN_DIR:=bin
-LIB_DIR:=lib
-SRC_DIR=src
-INC_DIR:=include
-OBJ_DIR:=obj
-
-LIB =		libvcflib.a
-SOVERSION =	1
-SLIB =		libvcflib.so.$(SOVERSION)
-
-# TODO
-#vcfstats.cpp
-
-BIN_SOURCES = src/vcfecho.cpp \
-			  src/vcfnormalizesvs.cpp \
-			  src/dumpContigsFromHeader.cpp \
-			  src/bFst.cpp \
-			  src/pVst.cpp \
-			  src/hapLrt.cpp \
-			  src/popStats.cpp \
-			  src/wcFst.cpp \
-			  src/iHS.cpp \
-			  src/segmentFst.cpp \
-			  src/segmentIhs.cpp \
-			  src/genotypeSummary.cpp \
-			  src/sequenceDiversity.cpp \
-			  src/pFst.cpp \
-			  src/smoother.cpp \
-			  src/LD.cpp \
-			  src/plotHaps.cpp \
-			  src/abba-baba.cpp \
-			  src/permuteGPAT++.cpp \
-			  src/permuteSmooth.cpp \
-			  src/normalize-iHS.cpp \
-			  src/meltEHH.cpp \
-			  src/vcfaltcount.cpp \
-			  src/vcfhetcount.cpp \
-			  src/vcfhethomratio.cpp \
-			  src/vcffilter.cpp \
-			  src/vcf2tsv.cpp \
-			  src/vcfgenotypes.cpp \
-			  src/vcfannotategenotypes.cpp \
-			  src/vcfcommonsamples.cpp \
-			  src/vcfremovesamples.cpp \
-			  src/vcfkeepsamples.cpp \
-			  src/vcfsamplenames.cpp \
-			  src/vcfgenotypecompare.cpp \
-			  src/vcffixup.cpp \
-			  src/vcfclassify.cpp \
-			  src/vcfsamplediff.cpp \
-			  src/vcfremoveaberrantgenotypes.cpp \
-			  src/vcfrandom.cpp \
-			  src/vcfparsealts.cpp \
-			  src/vcfstats.cpp \
-			  src/vcfflatten.cpp \
-			  src/vcfprimers.cpp \
-			  src/vcfnumalt.cpp \
-			  src/vcfcleancomplex.cpp \
-			  src/vcfintersect.cpp \
-			  src/vcfannotate.cpp \
-			  src/vcfallelicprimitives.cpp \
-			  src/vcfoverlay.cpp \
-			  src/vcfaddinfo.cpp \
-			  src/vcfkeepinfo.cpp \
-			  src/vcfkeepgeno.cpp \
-			  src/vcfafpath.cpp \
-			  src/vcfcountalleles.cpp \
-			  src/vcflength.cpp \
-			  src/vcfdistance.cpp \
-			  src/vcfrandomsample.cpp \
-			  src/vcfentropy.cpp \
-			  src/vcfglxgt.cpp \
-			  src/vcfroc.cpp \
-			  src/vcfcheck.cpp \
-			  src/vcfstreamsort.cpp \
-			  src/vcfuniq.cpp \
-			  src/vcfuniqalleles.cpp \
-			  src/vcfremap.cpp \
-			  src/vcf2fasta.cpp \
-			  src/vcfsitesummarize.cpp \
-			  src/vcfbreakmulti.cpp \
-			  src/vcfcreatemulti.cpp \
-			  src/vcfevenregions.cpp \
-			  src/vcfcat.cpp \
-			  src/vcfgenosummarize.cpp \
-			  src/vcfgenosamplenames.cpp \
-			  src/vcfgeno2haplo.cpp \
-			  src/vcfleftalign.cpp \
-			  src/vcfcombine.cpp \
-			  src/vcfgeno2alleles.cpp \
-			  src/vcfindex.cpp \
-			  src/vcf2dag.cpp \
-			  src/vcfsample2info.cpp \
-			  src/vcfqual2info.cpp \
-			  src/vcfinfo2qual.cpp \
-			  src/vcfglbound.cpp \
-			  src/vcfunphase.cpp \
-			  src/vcfnull2ref.cpp \
-			  src/vcfinfosummarize.cpp
-
-# when we can figure out how to build on mac
-# src/vcfsom.cpp
-
-#BINS = $(BIN_SOURCES:.cpp=)
-BINS = $(addprefix bin/,$(notdir $(BIN_SOURCES:.cpp=)))
-SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
-# Use ?= to allow overriding from the env or command-line.
-
-MAKE ?=		make
-LOCALBASE ?=	/usr/local
-LIB_PATH ?=	${LOCALBASE}/lib
-
-CC ?=		cc
-CXX ?=		c++
-CXXFLAGS ?=	-O3
-CFLAGS +=	-D_FILE_OFFSET_BITS=64 -fPIC
-CXXFLAGS +=	$(CFLAGS) --std=c++11
-#CXXFLAGS +=	-pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
-
-DESTDIR ?=	stage
-PREFIX ?=	/usr/local
-STRIP ?=	strip
-INSTALL ?=	install -c
-MKDIR ?=	mkdir -p
-AR ?=		ar
-
-SSW =		src/ssw.o src/ssw_cpp.o
-
-INCLUDES =	-I${LOCALBASE}/include \
-		-I${LOCALBASE}/include/smithwaterman \
-		-I${LOCALBASE}/include/multichoose \
-		-I${LOCALBASE}/include/fastahack \
-		-I${LOCALBASE}/include/intervaltree
-LDFLAGS +=	-L. -lvcflib \
-		-L$(LIB_PATH) -lsw -ltabix -lhts -lfastahack -lfilevercmp \
-		-lpthread -lz -lm
-
-all: $(OBJECTS) $(BINS) $(LIB) $(SLIB)
-
-ssw.o:		src/ssw.h
-ssw_cpp.o:	src/ssw_cpp.h
-
-openmp:
-	$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
-
-profiling:
-	$(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all
-
-gprof:
-	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
-
-$(OBJECTS): $(SOURCES) $(HEADERS)
-	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(CXXFLAGS)
-
-$(SHORTBINS):
-	$(MAKE) $(BIN_DIR)/$@
-
-$(BINS): $(BIN_SOURCES) $(LIB) $(OBJECTS) $(SSW) pre
-	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(CXXFLAGS) $(LDFLAGS)
-
-$(LIB): $(OBJECTS) $(SSW)
-	ar rs $(LIB) $(OBJECTS) $(SSW)
-
-$(SLIB): $(OBJECTS) $(SSW)
-	$(CXX) -shared -Wl,-soname,$(SLIB) -o $(SLIB) $(OBJECTS) $(SSW)
-
-install: all
-	$(MKDIR) $(DESTDIR)$(PREFIX)/bin
-	$(MKDIR) $(DESTDIR)$(PREFIX)/include/vcflib
-	$(MKDIR) $(DESTDIR)$(PREFIX)/lib
-	$(INSTALL) bin/* $(DESTDIR)$(PREFIX)/bin
-	$(INSTALL) src/*.h src/*.hpp $(DESTDIR)$(PREFIX)/include/vcflib
-	$(INSTALL) $(LIB) $(SLIB) $(DESTDIR)$(PREFIX)/lib
-
-install-strip: install
-	$(STRIP) $(DESTDIR)$(PREFIX)/bin/* $(DESTDIR)$(PREFIX)/lib/$(SLIB)
-
-test: $(BINS)
-	@prove -Itests/lib -w tests/*.t
-
-clean:
-	rm -f $(BINS) $(OBJECTS)
-	rm -f ssw_cpp.o ssw.o
-	rm -f $(LIB)
-	rm -rf $(BIN_DIR)
-
-pre:
-	mkdir -p $(BIN_DIR)
-
-.PHONY: clean all test pre
diff --git a/biology/vcflib/files/Makefile.submod b/biology/vcflib/files/Makefile.submod
deleted file mode 100644
index aafad2809a9e..000000000000
--- a/biology/vcflib/files/Makefile.submod
+++ /dev/null
@@ -1,117 +0,0 @@
-#OBJ_DIR = ./
-HEADERS = src/Variant.h \
-		  src/split.h \
-		  src/join.h
-SOURCES = src/Variant.cpp \
-		  src/split.cpp
-OBJECTS= $(SOURCES:.cpp=.o)
-
-VCF_LIB_LOCAL:=$(shell pwd)
-BIN_DIR:=bin
-LIB_DIR:=lib
-SRC_DIR=src
-INC_DIR:=include
-OBJ_DIR:=obj
-
-include Makefile.common
-
-TABIX = tabixpp/tabix.o
-FASTAHACK = fastahack/Fasta.o
-SMITHWATERMAN = smithwaterman/SmithWatermanGotoh.o
-REPEATS = smithwaterman/Repeats.o
-INDELALLELE = smithwaterman/IndelAllele.o
-DISORDER = smithwaterman/disorder.o
-LEFTALIGN = smithwaterman/LeftAlign.o
-FSOM = fsom/fsom.o
-FILEVERCMP = filevercmp/filevercmp.o
-
-INCLUDES = -Itabixpp/htslib -I$(INC_DIR) -L. -Ltabixpp/htslib
-LDFLAGS = -L$(LIB_DIR) -lvcflib -lhts -lpthread -lz -lm
-
-
-all: $(OBJECTS) $(BINS)
-
-CXX ?= c++
-CXXFLAGS ?= -O3 -D_FILE_OFFSET_BITS=64
-#CXXFLAGS = -O2
-#CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
-
-SSW = src/ssw.o src/ssw_cpp.o
-
-ssw.o: src/ssw.h
-ssw_cpp.o:src/ssw_cpp.h
-
-openmp:
-	$(MAKE) CXXFLAGS="$(CXXFLAGS) -fopenmp -D HAS_OPENMP"
-
-profiling:
-	$(MAKE) CXXFLAGS="$(CXXFLAGS) -g" all
-
-gprof:
-	$(MAKE) CXXFLAGS="$(CXXFLAGS) -pg" all
-
-$(OBJECTS): $(SOURCES) $(HEADERS) $(TABIX) multichoose pre $(SMITHWATERMAN) $(FILEVERCMP)
-	$(CXX) -c -o $@ src/$(*F).cpp $(INCLUDES) $(LDFLAGS) $(CXXFLAGS) && cp src/*.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
-multichoose: pre
-	cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
-intervaltree: pre
-	cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
-$(TABIX): pre
-	cd tabixpp && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
-$(SMITHWATERMAN): pre
-	cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
-
-$(DISORDER): $(SMITHWATERMAN)
-
-$(REPEATS): $(SMITHWATERMAN)
-
-$(LEFTALIGN): $(SMITHWATERMAN)
-
-$(INDELALLELE): $(SMITHWATERMAN)
-
-$(FASTAHACK): pre
-	cd fastahack && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
-
-#$(FSOM):
-#	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
-
-$(FILEVERCMP): pre
-	cd filevercmp && make && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/
-
-$(SHORTBINS): pre
-	$(MAKE) bin/$@
-
-$(BINS): $(BIN_SOURCES) libvcflib.a $(OBJECTS) $(SMITHWATERMAN) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) pre intervaltree
-	$(CXX) src/$(notdir $@).cpp -o $@ $(INCLUDES) $(LDFLAGS) $(CXXFLAGS)
-
-libvcflib.a: $(OBJECTS) $(SMITHWATERMAN) $(REPEATS) $(FASTAHACK) $(DISORDER) $(LEFTALIGN) $(INDELALLELE) $(SSW) $(FILEVERCMP) $(TABIX) pre
-	ar rs libvcflib.a $(OBJECTS) smithwaterman/sw.o $(FASTAHACK) $(SSW) $(FILEVERCMP) $(TABIX)
-	cp libvcflib.a $(LIB_DIR)
-
-
-test: $(BINS)
-	@prove -Itests/lib -w tests/*.t
-
-pre:
-	if [ ! -d $(BIN_DIR) ]; then mkdir -p $(BIN_DIR); fi
-	if [ ! -d $(LIB_DIR) ]; then mkdir -p $(LIB_DIR); fi
-	if [ ! -d $(INC_DIR) ]; then mkdir -p $(INC_DIR); fi
-	if [ ! -d $(OBJ_DIR) ]; then mkdir -p $(OBJ_DIR); fi
-
-clean:
-	rm -f $(BINS) $(OBJECTS)
-	rm -f ssw_cpp.o ssw.o
-	rm -f libvcflib.a
-	rm -rf $(BIN_DIR)
-	rm -rf $(LIB_DIR)
-	rm -rf $(INC_DIR)
-	rm -rf $(OBJ_DIR)
-	cd tabixpp && make clean
-	cd smithwaterman && make clean
-	cd fastahack && make clean
-
-.PHONY: clean all test pre
diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..2520c928273e
--- /dev/null
+++ b/biology/vcflib/files/patch-CMakeLists.txt
@@ -0,0 +1,11 @@
+--- CMakeLists.txt.orig	2021-11-03 15:07:33 UTC
++++ CMakeLists.txt
+@@ -230,7 +230,7 @@ if (NOT BUILD_ONLY_LIB)
+   foreach(BIN ${BINS})
+     add_executable(${BIN} src/${BIN}.cpp)
+     target_include_directories(${BIN} PUBLIC ${TABIXPP_LIBRARIES} ${HTSLIB_INCLUDE_DIRS})
+-    target_link_libraries(${BIN} vcflib tabixpp -DGIT_VERSION=0.9.0 ${TABIXPP_LIBRARIES} ${HTSLIB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${LIBLZMA_LIBRARIES} ${BZIP2_LIBRARIES})
++    target_link_libraries(${BIN} vcflib tabix -DGIT_VERSION=0.9.0 ${TABIXPP_LIBRARIES} ${HTSLIB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${LIBLZMA_LIBRARIES} ${BZIP2_LIBRARIES})
+   endforeach(BIN ${BINS})
+   install(TARGETS ${BINS} RUNTIME DESTINATION bin)
+ endif()
diff --git a/biology/vcflib/files/patch-src_cdflib.cpp b/biology/vcflib/files/patch-src_cdflib.cpp
deleted file mode 100644
index 84bff432c1ed..000000000000
--- a/biology/vcflib/files/patch-src_cdflib.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/cdflib.cpp.orig	2018-03-09 20:31:19 UTC
-+++ src/cdflib.cpp
-@@ -10040,7 +10040,7 @@ void negative_binomial_cdf_values ( int 
-     1, 2, 3,
-     0, 1, 2 };
- 
--  if ( n_data < 0 )
-+  if ( *n_data < 0 )
-   {
-     *n_data = 0;
-   }
diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist
index 944045d78581..4aa9ba414bd3 100644
--- a/biology/vcflib/pkg-plist
+++ b/biology/vcflib/pkg-plist
@@ -1,4 +1,3 @@
-bin/LD
 bin/abba-baba
 bin/bFst
 bin/dumpContigsFromHeader
@@ -59,10 +58,9 @@ bin/vcfintersect
 bin/vcfkeepgeno
 bin/vcfkeepinfo
 bin/vcfkeepsamples
+bin/vcfld
 bin/vcfleftalign
 bin/vcflength
-bin/vcfnormalizesvs
-bin/vcfnull2ref
 bin/vcfnumalt
 bin/vcfoverlay
 bin/vcfparsealts
@@ -82,23 +80,119 @@ bin/vcfstats
 bin/vcfstreamsort
 bin/vcfuniq
 bin/vcfuniqalleles
-bin/vcfunphase
 bin/wcFst
-include/vcflib/BedReader.h
-include/vcflib/Variant.h
-include/vcflib/cdflib.hpp
-include/vcflib/convert.h
-include/vcflib/gpatInfo.hpp
-include/vcflib/join.h
-include/vcflib/mt19937ar.h
-include/vcflib/pdflib.hpp
-include/vcflib/rnglib.hpp
-include/vcflib/split.h
-include/vcflib/ssw.hpp
-include/vcflib/ssw_cpp.hpp
-include/vcflib/var.hpp
-include/vcflib/vec128int.h
-include/vcflib/veclib_types.h
+include/BandedSmithWaterman.h
+include/BedReader.h
+include/Fasta.h
+include/IndelAllele.h
+include/IntervalTree.h
+include/LargeFileSupport.h
+include/LeftAlign.h
+include/Mosaik.h
+include/Region.h
+include/Repeats.h
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