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-rw-r--r--vcpkg/ports/htslib/0001-set-linkage.patch29
-rw-r--r--vcpkg/ports/htslib/0002-pthread-flag.patch78
-rw-r--r--vcpkg/ports/htslib/0003-no-tests.patch13
-rw-r--r--vcpkg/ports/htslib/0004-fix-find-htscodecs.patch22
-rw-r--r--vcpkg/ports/htslib/bzip2-use-pkgconfig.diff31
-rw-r--r--vcpkg/ports/htslib/portfile.cmake54
-rw-r--r--vcpkg/ports/htslib/vcpkg.json32
7 files changed, 259 insertions, 0 deletions
diff --git a/vcpkg/ports/htslib/0001-set-linkage.patch b/vcpkg/ports/htslib/0001-set-linkage.patch
new file mode 100644
index 0000000..066b145
--- /dev/null
+++ b/vcpkg/ports/htslib/0001-set-linkage.patch
@@ -0,0 +1,29 @@
+diff --git a/Makefile b/Makefile
+index 0bbb078..e98f287 100644
+--- a/Makefile
++++ b/Makefile
+@@ -958,11 +958,10 @@ $(srcprefix)htslib.map: libhts.so
+ rm -f $@.tmp ; \
+ fi
+
+-install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(REF_CACHE_PROGRAMS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
++install: $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-pkgconfig
+ $(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(REF_CACHE_PROGRAMS) $(DESTDIR)$(bindir)
+ if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
+ $(INSTALL_DATA) $(SRC)htslib/*.h $(DESTDIR)$(includedir)/htslib
+- $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
+ $(INSTALL_MAN) $(SRC)annot-tsv.1 $(SRC)bgzip.1 $(SRC)htsfile.1 $(SRC)tabix.1 $(DESTDIR)$(man1dir)
+ if test "x$(REF_CACHE_PROGRAMS)" != "x" ; then \
+ $(INSTALL_MAN) $(SRC)ref_cache/ref-cache.1 $(DESTDIR)$(man1dir) ; \
+@@ -970,6 +969,11 @@ install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(REF_CACHE_PROGRAMS) insta
+ $(INSTALL_MAN) $(SRC)faidx.5 $(SRC)sam.5 $(SRC)vcf.5 $(DESTDIR)$(man5dir)
+ $(INSTALL_MAN) $(SRC)htslib-s3-plugin.7 $(DESTDIR)$(man7dir)
+
++install-static: install
++ $(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
++
++install-dynamic: install install-$(SHLIB_FLAVOUR)
++
+ installdirs:
+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(man7dir) $(DESTDIR)$(pkgconfigdir)
+ if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi
diff --git a/vcpkg/ports/htslib/0002-pthread-flag.patch b/vcpkg/ports/htslib/0002-pthread-flag.patch
new file mode 100644
index 0000000..d94dd0a
--- /dev/null
+++ b/vcpkg/ports/htslib/0002-pthread-flag.patch
@@ -0,0 +1,78 @@
+diff --git a/Makefile b/Makefile
+index e98f287..ab3fdc1 100644
+--- a/Makefile
++++ b/Makefile
+@@ -145,6 +145,8 @@ HTS_BUILD_AVX2 =
+ HTS_BUILD_AVX512 =
+ HTS_BUILD_SSE4 =
+
++PTHREAD = -pthread
++
+ include htslib_vars.mk
+ include htscodecs.mk
+
+@@ -191,10 +193,10 @@ config_vars.h:
+ .SUFFIXES: .bundle .c .cygdll .dll .o .pico .so
+
+ .c.o:
+- $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
++ $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(PTHREAD) -c -o $@ $<
+
+ .c.pico:
+- $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
++ $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(PTHREAD) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
+
+ ref_cache/%.o: ref_cache/%.c
+ $(CC) $(CFLAGS) $(REF_CACHE_EXTRA_C_FLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
+@@ -409,7 +411,7 @@ print-config:
+ # file used at runtime (when $LD_LIBRARY_PATH includes the build directory).
+
+ libhts.so: $(LIBHTS_OBJS:.o=.pico)
+- $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(VERSION_SCRIPT_LDFLAGS) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) -lpthread
++ $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(VERSION_SCRIPT_LDFLAGS) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) $(PTHREAD)
+ ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
+
+ # Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
+@@ -421,10 +423,10 @@ libhts.dylib: $(LIBHTS_OBJS)
+ ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
+
+ cyghts-$(LIBHTS_SOVERSION).dll libhts.dll.a: $(LIBHTS_OBJS)
+- $(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
++ $(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) $(PTHREAD)
+
+ hts-$(LIBHTS_SOVERSION).dll hts.dll.a: $(LIBHTS_OBJS)
+- $(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread
++ $(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) $(PTHREAD)
+
+ hts-$(LIBHTS_SOVERSION).def: hts-$(LIBHTS_SOVERSION).dll
+ gendef hts-$(LIBHTS_SOVERSION).dll
+@@ -471,7 +473,7 @@ hts-object-files: $(LIBHTS_OBJS)
+ # may not be able to access libhts symbols via the main program's libhts
+ # if that was dynamically loaded without an explicit RTLD_GLOBAL.
+ %.so: %.pico libhts.so
+- $(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< libhts.so $(LIBS) -lpthread
++ $(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< libhts.so $(LIBS) $(PTHREAD)
+
+ # For programs *statically* linked to libhts.a, on macOS loading a plugin
+ # linked to a shared libhts.NN.dylib would lead to conflicting duplicate
+@@ -553,16 +555,16 @@ htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static3
+ htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico: TARGET_CFLAGS = $(HTS_CFLAGS_SSE4)
+
+ annot-tsv: annot-tsv.o libhts.a
+- $(CC) $(LDFLAGS) -o $@ annot-tsv.o libhts.a $(LIBS) -lpthread
++ $(CC) $(LDFLAGS) -o $@ annot-tsv.o libhts.a $(LIBS) $(PTHREAD)
+
+ bgzip: bgzip.o libhts.a
+- $(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) -lpthread
++ $(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) $(PTHREAD)
+
+ htsfile: htsfile.o libhts.a
+- $(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) -lpthread
++ $(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) $(PTHREAD)
+
+ tabix: tabix.o libhts.a
+- $(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread
++ $(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) $(PTHREAD)
+
+ ref_cache/ref-cache: $(REF_CACHE_OBJS)
+ $(CC) $(LDFLAGS) $(REF_CACHE_EXTRA_LD_FLAGS) -o $@ $(REF_CACHE_OBJS) -lcurl
diff --git a/vcpkg/ports/htslib/0003-no-tests.patch b/vcpkg/ports/htslib/0003-no-tests.patch
new file mode 100644
index 0000000..1e8e49d
--- /dev/null
+++ b/vcpkg/ports/htslib/0003-no-tests.patch
@@ -0,0 +1,13 @@
+diff --git a/Makefile b/Makefile
+index fb4f527..751df4b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -111,7 +111,7 @@ BUILT_THRASH_PROGRAMS = \
+ test/thrash_threads6 \
+ test/thrash_threads7
+
+ all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \
+- $(BUILT_TEST_PROGRAMS) htslib_static.mk htslib-uninstalled.pc
++ htslib_static.mk htslib-uninstalled.pc
+
+ # Report compiler and version
diff --git a/vcpkg/ports/htslib/0004-fix-find-htscodecs.patch b/vcpkg/ports/htslib/0004-fix-find-htscodecs.patch
new file mode 100644
index 0000000..4fc6e2d
--- /dev/null
+++ b/vcpkg/ports/htslib/0004-fix-find-htscodecs.patch
@@ -0,0 +1,22 @@
+diff --git a/configure.ac b/configure.ac
+index 49f2cbc..434086f 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -156,7 +156,7 @@ m4_ifdef([PKG_PROG_PKG_CONFIG], [PKG_PROG_PKG_CONFIG], [PKG_CONFIG=""])
+ need_crypto=no
+ pc_requires=
+ static_LDFLAGS=$LDFLAGS
+-static_LIBS='-lpthread -lz -lm'
++static_LIBS='-pthread -lz -lm'
+ private_LIBS=$LDFLAGS
+
+ AC_ARG_ENABLE([versioned-symbols],
+@@ -404,7 +404,7 @@ AS_IF([test "x$with_external_htscodecs" != "xno"],
+ AC_CHECK_HEADER([htscodecs/rANS_static4x16.h],[],
+ [libhtscodecs='missing header'],[;])
+ AC_CHECK_LIB([htscodecs],[rans_compress_bound_4x16],
+- [:],[libhtscodecs='missing library'])
++ [:],[libhtscodecs='missing library'], ["$static_LIBS"])
+ AS_IF([test "$libhtscodecs" = "ok"],
+ [AC_DEFINE([HAVE_EXTERNAL_LIBHTSCODECS], 1, [Define if using an external libhtscodecs])
+ LIBS="-lhtscodecs $LIBS"
diff --git a/vcpkg/ports/htslib/bzip2-use-pkgconfig.diff b/vcpkg/ports/htslib/bzip2-use-pkgconfig.diff
new file mode 100644
index 0000000..34d7bc8
--- /dev/null
+++ b/vcpkg/ports/htslib/bzip2-use-pkgconfig.diff
@@ -0,0 +1,31 @@
+diff --git a/configure.ac b/configure.ac
+index 593a664..5fcca0d 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -412,8 +412,11 @@ fi],
+
+ if test "$enable_bz2" != no; then
+ bz2_devel=ok
+- AC_CHECK_HEADER([bzlib.h], [], [bz2_devel=missing], [;])
+- AC_CHECK_LIB([bz2], [BZ2_bzBuffToBuffCompress], [], [bz2_devel=missing])
++ PKG_CHECK_MODULES([BZ2_PKG], [bzip2], [
++ AC_DEFINE([HAVE_LIBBZ2], 1, [Define if libbzip2 is available.])
++ LIBS="$LIBS $BZ2_PKG_LIBS"
++ CFLAGS="$CFLAGS $BZ2_PKG_CFLAGS"
++ ], [bz2_devel=missing])
+ if test $bz2_devel != ok; then
+ MSG_ERROR([libbzip2 development files not found
+
+@@ -430,12 +433,7 @@ produced elsewhere unreadable) or resolve this error to build HTSlib.])
+ fi
+ dnl Unfortunately the 'bzip2' package-cfg module is not standard.
+ dnl Redhat/Fedora has it; Debian/Ubuntu does not.
+- if test -n "$PKG_CONFIG" && "$PKG_CONFIG" --exists bzip2; then
+ pc_requires="$pc_requires bzip2"
+- else
+- private_LIBS="$private_LIBS -lbz2"
+- fi
+- static_LIBS="$static_LIBS -lbz2"
+ fi
+
+ if test "$enable_lzma" != no; then
diff --git a/vcpkg/ports/htslib/portfile.cmake b/vcpkg/ports/htslib/portfile.cmake
new file mode 100644
index 0000000..736bd3f
--- /dev/null
+++ b/vcpkg/ports/htslib/portfile.cmake
@@ -0,0 +1,54 @@
+vcpkg_from_github(
+ OUT_SOURCE_PATH SOURCE_PATH
+ REPO samtools/htslib
+ REF "${VERSION}"
+ SHA512 3537149d4118bf27424845a44fdfdb5ffce2376bf956ba15cd61686b84efa320c66fed76eab2fc381f344d61607f7e63494fdd6ef8cf4e40cdb3ac6fe29f86ad
+ HEAD_REF develop
+ PATCHES
+ 0001-set-linkage.patch
+ 0002-pthread-flag.patch
+ 0003-no-tests.patch
+ 0004-fix-find-htscodecs.patch
+ bzip2-use-pkgconfig.diff
+)
+
+set(FEATURE_OPTIONS "")
+
+macro(enable_feature feature switch)
+ if("${feature}" IN_LIST FEATURES)
+ list(APPEND FEATURE_OPTIONS "--enable-${switch}")
+ else()
+ list(APPEND FEATURE_OPTIONS "--disable-${switch}")
+ endif()
+endmacro()
+
+enable_feature("bzip2" "bz2")
+enable_feature("lzma" "lzma")
+
+if("deflate" IN_LIST FEATURES)
+ list(APPEND FEATURE_OPTIONS "--with-libdeflate")
+else()
+ list(APPEND FEATURE_OPTIONS "--without-libdeflate")
+endif()
+
+vcpkg_configure_make(
+ AUTOCONFIG
+ SOURCE_PATH "${SOURCE_PATH}"
+ OPTIONS
+ --with-external-htscodecs
+ --disable-libcurl
+ --disable-gcs
+ --disable-s3
+ --disable-plugins
+ ${FEATURE_OPTIONS}
+)
+
+vcpkg_install_make(
+ INSTALL_TARGET install-${VCPKG_LIBRARY_LINKAGE}
+)
+
+file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/share")
+
+vcpkg_fixup_pkgconfig()
+
+vcpkg_install_copyright(FILE_LIST "${SOURCE_PATH}/LICENSE")
diff --git a/vcpkg/ports/htslib/vcpkg.json b/vcpkg/ports/htslib/vcpkg.json
new file mode 100644
index 0000000..a958019
--- /dev/null
+++ b/vcpkg/ports/htslib/vcpkg.json
@@ -0,0 +1,32 @@
+{
+ "name": "htslib",
+ "version": "1.22.1",
+ "description": "C library for high-throughput sequencing data formats",
+ "homepage": "https://github.com/samtools/htslib",
+ "license": "MIT",
+ "supports": "!windows",
+ "dependencies": [
+ "htscodecs",
+ "zlib"
+ ],
+ "features": {
+ "bzip2": {
+ "description": "Enable support for BZ2-compressed CRAM files",
+ "dependencies": [
+ "bzip2"
+ ]
+ },
+ "deflate": {
+ "description": "Use libdeflate for faster crc and deflate algorithms",
+ "dependencies": [
+ "libdeflate"
+ ]
+ },
+ "lzma": {
+ "description": "Enable support for LZMA-compressed CRAM files",
+ "dependencies": [
+ "liblzma"
+ ]
+ }
+ }
+}
generated by cgit v1.2.3 (git 2.39.1) at 2026-02-15 06:24:53 +0000