[htslib] update to 1.22.1 (#48178)

2025-11-08 09:01:01 +09:00 · 2025-11-08 09:01:01 +09:00 · 32c84a3684
parent d805610238
commit 32c84a3684
7 changed files with 27 additions and 32 deletions
--- a/ports/htslib/0001-set-linkage.patch
+++ b/ports/htslib/0001-set-linkage.patch
@ -1,18 +1,21 @@
 diff --git a/Makefile b/Makefile
-index 99142c8..97cd369 100644
+index 0bbb078..e98f287 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -857,15 +857,19 @@ $(srcprefix)htslib.map: libhts.so
+@@ -958,11 +958,10 @@ $(srcprefix)htslib.map: libhts.so
 	    rm -f $@.tmp ; \
 	fi
 
-install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
+-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) $(DESTDIR)$(bindir)
+ 	$(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)
 
--- a/ports/htslib/0002-pthread-flag.patch
+++ b/ports/htslib/0002-pthread-flag.patch
@ -1,8 +1,8 @@
 diff --git a/Makefile b/Makefile
-index f6e154f..fb4f527 100644
+index e98f287..ab3fdc1 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -137,6 +137,8 @@ HTS_BUILD_AVX2 =
+@@ -145,6 +145,8 @@ HTS_BUILD_AVX2 =
 HTS_BUILD_AVX512 =
 HTS_BUILD_SSE4 =
 
@ -11,7 +11,7 @@ index f6e154f..fb4f527 100644
 include htslib_vars.mk
 include htscodecs.mk
 
-@@ -183,10 +185,10 @@ config_vars.h:
+@@ -191,10 +193,10 @@ config_vars.h:
 .SUFFIXES: .bundle .c .cygdll .dll .o .pico .so
 
 .c.o:
@ -22,9 +22,9 @@ index f6e154f..fb4f527 100644
 -	$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
 +	$(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(PTHREAD) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
 
- 
- LIBHTS_OBJS = \
-@@ -358,7 +360,7 @@ print-config:
+ 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)
@ -33,7 +33,7 @@ index f6e154f..fb4f527 100644
 	ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
 
 # Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
-@@ -370,10 +372,10 @@ libhts.dylib: $(LIBHTS_OBJS)
+@@ -421,10 +423,10 @@ libhts.dylib: $(LIBHTS_OBJS)
 	ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
 
 cyghts-$(LIBHTS_SOVERSION).dll libhts.dll.a: $(LIBHTS_OBJS)
@ -46,7 +46,7 @@ index f6e154f..fb4f527 100644
 
 hts-$(LIBHTS_SOVERSION).def: hts-$(LIBHTS_SOVERSION).dll
 	gendef hts-$(LIBHTS_SOVERSION).dll
-@@ -420,7 +422,7 @@ hts-object-files: $(LIBHTS_OBJS)
+@@ -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
@ -55,7 +55,7 @@ index f6e154f..fb4f527 100644
 
 # For programs *statically* linked to libhts.a, on macOS loading a plugin
 # linked to a shared libhts.NN.dylib would lead to conflicting duplicate
-@@ -501,16 +503,16 @@ htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static3
+@@ -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
@ -74,5 +74,5 @@ index f6e154f..fb4f527 100644
 -	$(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread
 +	$(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) $(PTHREAD)
 
- annot-tsv.o: annot-tsv.c config.h $(htslib_hts_h) $(htslib_hts_defs_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_regidx_h) $(textutils_internal_h)
- bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_hfile_h)
+ ref_cache/ref-cache: $(REF_CACHE_OBJS)
+ 	$(CC) $(LDFLAGS) $(REF_CACHE_EXTRA_LD_FLAGS) -o $@ $(REF_CACHE_OBJS) -lcurl
--- a/ports/htslib/0005-remove-duplicate-lhts.patch
+++ b/ports/htslib/0005-remove-duplicate-lhts.patch
@ -1,11 +0,0 @@
-diff --git a/htslib.pc.in b/htslib.pc.in
-index d969d6b..fdeeba9 100644
--- a/htslib.pc.in
-+++ b/htslib.pc.in
-@@ -11,5 +11,5 @@ Description: C library for high-throughput sequencing data formats
- Version: @-PACKAGE_VERSION@
- Cflags: -I${includedir}
- Libs: -L${libdir} -lhts
-Libs.private: -L${libdir} @private_LIBS@ -lhts -lm -lpthread
-+Libs.private: -L${libdir} @private_LIBS@ -lm -lpthread
- Requires.private: zlib @pc_requires@
--- a/ports/htslib/portfile.cmake
+++ b/ports/htslib/portfile.cmake
@ -2,14 +2,13 @@ vcpkg_from_github(
    OUT_SOURCE_PATH SOURCE_PATH
    REPO samtools/htslib
    REF "${VERSION}"
-    SHA512 6df1a493ac9f13cae5a510537bdf83aa9635a79efe635b8a5a5cbd89345c75c9a42e686c4f0497761ddfad3b86a9814ed35ba2ac340d0f1c7b5e2e186b152875
+    SHA512 3537149d4118bf27424845a44fdfdb5ffce2376bf956ba15cd61686b84efa320c66fed76eab2fc381f344d61607f7e63494fdd6ef8cf4e40cdb3ac6fe29f86ad
    HEAD_REF develop
    PATCHES
        0001-set-linkage.patch
        0002-pthread-flag.patch
        0003-no-tests.patch
        0004-fix-find-htscodecs.patch
-        0005-remove-duplicate-lhts.patch # https://github.com/samtools/htslib/pull/1852
        bzip2-use-pkgconfig.diff
 )

--- a/ports/htslib/vcpkg.json
+++ b/ports/htslib/vcpkg.json
@ -1,7 +1,6 @@
 {
  "name": "htslib",
-  "version": "1.21",
-  "port-version": 2,
+  "version": "1.22.1",
  "description": "C library for high-throughput sequencing data formats",
  "homepage": "https://github.com/samtools/htslib",
  "license": "MIT",
--- a/versions/baseline.json
+++ b/versions/baseline.json
@ -3805,8 +3805,8 @@
      "port-version": 0
    },
    "htslib": {
-      "baseline": "1.21",
-      "port-version": 2
+      "baseline": "1.22.1",
+      "port-version": 0
    },
    "http-parser": {
      "baseline": "2.9.4",
--- a/versions/h-/htslib.json
+++ b/versions/h-/htslib.json
@ -1,5 +1,10 @@
 {
  "versions": [
+    {
+      "git-tree": "494ffb1a8f9ed145a2b89295a532c585d22eaa71",
+      "version": "1.22.1",
+      "port-version": 0
+    },
    {
      "git-tree": "d5105fd911217d73a620694d12333e7e0282337a",
      "version": "1.21",