git: 39b2e62d29fa - main - biology/vcflib: Update to 1.0.13
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Date: Mon, 28 Apr 2025 11:43:09 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=39b2e62d29fa852537575f7088635564278e2778
commit 39b2e62d29fa852537575f7088635564278e2778
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-04-28 11:42:22 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-04-28 11:42:22 +0000
biology/vcflib: Update to 1.0.13
Bug fix release
Changes: https://github.com/vcflib/vcflib/releases
Reported by: portscout
---
biology/vcflib/Makefile | 5 +++--
biology/vcflib/distinfo | 6 +++---
biology/vcflib/files/patch-CMakeLists.txt | 16 +++++++++-------
biology/vcflib/pkg-plist | 13 ++++++++++---
4 files changed, 25 insertions(+), 15 deletions(-)
diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile
index f53800bfa2d7..ac8ea593cdfa 100644
--- a/biology/vcflib/Makefile
+++ b/biology/vcflib/Makefile
@@ -1,6 +1,6 @@
PORTNAME= vcflib
DISTVERSIONPREFIX= v
-DISTVERSION= 1.0.12
+DISTVERSION= 1.0.13
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
@@ -42,7 +42,8 @@ ZIG_DESC= Include Zig language support
ZIG_BUILD_DEPENDS= zig>0:lang/zig
-CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so.0
+CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so.0 \
+ -DTABIXPP_LOCAL=${WRKSRC}/contrib/tabixpp
ZIG_CMAKE_OFF= -DZIG=OFF
# Clang and GCC disable sse2 by default on i386, but it's required for vcflib
diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo
index 066030757d4d..f9a114d02cf4 100644
--- a/biology/vcflib/distinfo
+++ b/biology/vcflib/distinfo
@@ -1,6 +1,6 @@
-TIMESTAMP = 1732541764
-SHA256 (ekg-vcflib-v1.0.12_GH0.tar.gz) = 7ab5b6a87a39105107029f5e0da52ece612c71095ab2aec69a00320f44bc5300
-SIZE (ekg-vcflib-v1.0.12_GH0.tar.gz) = 23543176
+TIMESTAMP = 1745795908
+SHA256 (ekg-vcflib-v1.0.13_GH0.tar.gz) = ea062b6cf6b9074118bc949112b4f0d3fcc5edb58af9621f9acb92f08a452c55
+SIZE (ekg-vcflib-v1.0.13_GH0.tar.gz) = 23544091
SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
SHA256 (ekg-filevercmp-df20dcc_GH0.tar.gz) = d34bec614be638e05eb6fa419c936b9e7de58d50b1a096a5ca02aadb7db6b059
diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt
index 347b5a48ab73..695ac3940fd3 100644
--- a/biology/vcflib/files/patch-CMakeLists.txt
+++ b/biology/vcflib/files/patch-CMakeLists.txt
@@ -1,6 +1,6 @@
---- CMakeLists.txt.orig 2024-11-21 07:59:50 UTC
+--- CMakeLists.txt.orig 2025-04-24 23:28:09 UTC
+++ CMakeLists.txt
-@@ -70,7 +70,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release)
+@@ -68,7 +68,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release)
endif()
if (${CMAKE_BUILD_TYPE} MATCHES Release)
@@ -9,14 +9,16 @@
# set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast
endif()
-@@ -595,8 +595,8 @@ install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INS
+@@ -590,9 +590,9 @@ install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INS
# ---- Install
install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
--install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
-+# install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
+-if(WFA_GITMODULE)
+- install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
+-endif(WFA_GITMODULE)
++# if(WFA_GITMODULE)
++# install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
++# endif(WFA_GITMODULE)
install(FILES ${INCLUDES} DESTINATION include/vcflib)
--install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1)
-+install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1)
diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist
index 85671a488441..d5e562de28bf 100644
--- a/biology/vcflib/pkg-plist
+++ b/biology/vcflib/pkg-plist
@@ -26,6 +26,7 @@ bin/vcf2tsv
bin/vcf_strip_extra_headers
bin/vcfaddinfo
bin/vcfafpath
+bin/vcfallelicprimitives
bin/vcfaltcount
bin/vcfannotate
bin/vcfannotategenotypes
@@ -34,6 +35,7 @@ bin/vcfbreakmulti
bin/vcfcat
bin/vcfcheck
bin/vcfclassify
+bin/vcfcleancomplex
bin/vcfclearid
bin/vcfclearinfo
bin/vcfcombine
@@ -83,6 +85,7 @@ bin/vcfnulldotslashdot
bin/vcfnullgenofields
bin/vcfnumalt
bin/vcfoverlay
+bin/vcfparsealts
bin/vcfplotaltdiscrepancy.r
bin/vcfplotaltdiscrepancy.sh
bin/vcfplotsitediscrepancy.r
@@ -102,16 +105,19 @@ bin/vcfremap
bin/vcfremoveaberrantgenotypes
bin/vcfremovenonATGC
bin/vcfremovesamples
+bin/vcfroc
bin/vcfsample2info
bin/vcfsamplediff
bin/vcfsamplenames
bin/vcfsitesummarize
bin/vcfsnps
bin/vcfsort
+bin/vcfstats
bin/vcfstreamsort
bin/vcfuniq
bin/vcfuniqalleles
bin/vcfvarstats
+bin/vcfwave
bin/wcFst
include/vcflib/BandedSmithWaterman.h
include/vcflib/BedReader.h
@@ -127,7 +133,6 @@ include/vcflib/Repeats.h
include/vcflib/SmithWatermanGotoh.h
include/vcflib/Variant.h
include/vcflib/allele.hpp
-include/vcflib/canonicalize.h
include/vcflib/catch.hpp
include/vcflib/cdflib.hpp
include/vcflib/cigar.hpp
@@ -135,24 +140,26 @@ include/vcflib/convert.h
include/vcflib/disorder.h
include/vcflib/filevercmp.h
include/vcflib/gpatInfo.hpp
+include/vcflib/index.hpp
include/vcflib/join.h
include/vcflib/legacy.h
-include/vcflib/makeUnique.h
include/vcflib/mt19937ar.h
include/vcflib/multichoose.h
include/vcflib/murmur3.hpp
include/vcflib/pdflib.hpp
+include/vcflib/phase.hpp
include/vcflib/rkmh.hpp
include/vcflib/rnglib.hpp
include/vcflib/split.h
include/vcflib/ssw.hpp
include/vcflib/ssw_cpp.hpp
+include/vcflib/stats.hpp
+include/vcflib/tabix.hpp
include/vcflib/var.hpp
include/vcflib/vcf-c-api.h
include/vcflib/vcf-wfa.h
lib/libvcflib.a
lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so
-%%ZIG%%lib/libzig.a
share/man/man1/abba-baba.1.gz
share/man/man1/bFst.1.gz
share/man/man1/dumpContigsFromHeader.1.gz