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PORTNAME= freebayes
DISTVERSIONPREFIX= v
DISTVERSION= 1.3.6
PORTREVISION= 2
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping
WWW= https://github.com/ekg/freebayes
LICENSE= MIT
LIB_DEPENDS= libhts.so:biology/htslib
# Submodules use older versions than the ports, so we cannot safely unbundle
# No shared libs are built by the submodules so there will be no conflicts
# Yes, there are actually 2 versions of intervaltree required
USES= compiler:c++14-lang localbase meson perl5 pkgconfig
USE_GITHUB= yes
GH_ACCOUNT= ekg
GH_TUPLE= ekg:intervaltree:b90527f:intervaltree/vcflib/intervaltree \
ekg:vcflib:d4073c3:vcflib/vcflib-temp \
ekg:fastahack:bb33265:fastahack/vcflib/fastahack \
ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \
ekg:fsom:a6ef318:fsom/vcflib/fsom \
google:googletest:d225acc:googletest/vcflib/googletest \
ekg:intervaltree:17ddd57:intervaltree/vcflib/intervaltree \
edawson:libVCFH:615a06b:libVCFH/vcflib/libVCFH \
ekg:multichoose:68733cd:multichoose/vcflib/multichoose \
ekg:smithwaterman:2610e25:smithwaterman/vcflib/smithwaterman \
ekg:tabixpp:b255df1:tabixpp/vcflib/tabixpp \
simd-everywhere:simde-no-tests:2931676:simd/vcflib/src/simde \
ingydotnet:test-simple-bash:124673f:testsimplebash/test/test-simple-bash \
illusori:bash-tap:c38fbfa:bashtap/test/bash-tap
USE_PERL5= build
LDFLAGS+= -lexecinfo
PLIST_FILES= bin/bamleftalign bin/freebayes
# GH_TUPLEs cannot seem to share a top-level subdirectory, so we work around
# by dumping the parent in a temp directory and then moving the contents
post-extract:
${CP} -r ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
.include <bsd.port.mk>
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