[htslib, htscodecs] New ports

ports/htscodecs/0001-no-tests.patch

@@ -0,0 +1,13 @@
+diff --git a/tests/Makefile.am b/tests/Makefile.am
+index 873ad3e..0ab3638 100644
+--- a/tests/Makefile.am
++++ b/tests/Makefile.am
+@@ -31,7 +31,7 @@
+ # 
+
+ # Standalone test programs
+-noinst_PROGRAMS = rans4x16pr tokenise_name3 arith_dynamic rans4x8 rans4x16pr fqzcomp_qual varint entropy
++check_PROGRAMS = rans4x16pr tokenise_name3 arith_dynamic rans4x8 rans4x16pr fqzcomp_qual varint entropy
+
+ LDADD = $(top_builddir)/htscodecs/libhtscodecs.la
+ AM_CPPFLAGS = -I$(top_srcdir)

ports/htscodecs/portfile.cmake

@@ -0,0 +1,36 @@
+vcpkg_from_github(
+    OUT_SOURCE_PATH SOURCE_PATH
+    REPO samtools/htscodecs
+    REF "v${VERSION}"
+    SHA512 7533570b8b1cad0b9ed118170e5a9ff34fdde40b090f4ba3756f7899e2cd7230f8172425ecf6bd7b83b0b0b1a2a24f3d21795db7f0bc2c3add0a55342b970d1a
+    HEAD_REF master
+    PATCHES
+        0001-no-tests.patch # https://github.com/samtools/htscodecs/pull/120
+)
+
+set(FEATURE_OPTIONS "")
+
+macro(enable_feature feature switch)
+    if("${feature}" IN_LIST FEATURES)
+        list(APPEND FEATURE_OPTIONS "--enable-${switch}")
+    else()
+        list(APPEND FEATURE_OPTIONS "--disable-${switch}")
+    endif()
+endmacro()
+
+enable_feature("bzip2" "bz2")
+
+vcpkg_configure_make(
+    AUTOCONFIG
+    SOURCE_PATH "${SOURCE_PATH}"
+    OPTIONS
+        ${FEATURE_OPTIONS}
+)
+
+vcpkg_install_make()
+
+file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/share")
+
+vcpkg_fixup_pkgconfig()
+
+vcpkg_install_copyright(FILE_LIST "${SOURCE_PATH}/LICENSE.md")

ports/htscodecs/vcpkg.json

@@ -0,0 +1,16 @@
+{
+  "name": "htscodecs",
+  "version": "1.6.0",
+  "description": "Custom compression for CRAM and others.",
+  "homepage": "https://github.com/samtools/htscodecs",
+  "license": "MIT",
+  "supports": "!windows",
+  "features": {
+    "bzip2": {
+      "description": "Enable support for BZ2 within Arith streams",
+      "dependencies": [
+        "bzip2"
+      ]
+    }
+  }
+}

ports/htslib/0001-set-linkage.patch

@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index 99142c8..97cd369 100644
+--- a/Makefile
++++ b/Makefile
+@@ -857,15 +857,19 @@ $(srcprefix)htslib.map: libhts.so
+ 	    rm -f $@.tmp ; \
+ 	fi
+
+-install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
++install: $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-pkgconfig
+ 	$(INSTALL_PROGRAM) $(BUILT_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)
+ 	$(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

ports/htslib/0002-pthread-flag.patch

@@ -0,0 +1,78 @@
+diff --git a/Makefile b/Makefile
+index f6e154f..fb4f527 100644
+--- a/Makefile
++++ b/Makefile
+@@ -137,6 +137,8 @@ HTS_BUILD_AVX2 =
+ HTS_BUILD_AVX512 =
+ HTS_BUILD_SSE4 =
+
++PTHREAD = -pthread
++
+ include htslib_vars.mk
+ include htscodecs.mk
+
+@@ -183,10 +185,10 @@ 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 $@ $<
+
+
+ LIBHTS_OBJS = \
+@@ -358,7 +360,7 @@ 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
+@@ -370,10 +372,10 @@ 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
+@@ -420,7 +422,7 @@ 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
+@@ -501,16 +503,16 @@ 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)
+
+ 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)
+ bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_hfile_h)

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) \
++all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \
+      htslib_static.mk htslib-uninstalled.pc
+
+ ALL_CPPFLAGS = -I. $(CPPFLAGS)

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"

ports/htslib/portfile.cmake

@@ -0,0 +1,53 @@
+vcpkg_from_github(
+    OUT_SOURCE_PATH SOURCE_PATH
+    REPO samtools/htslib
+    REF "${VERSION}"
+    SHA512 b9de3769db6153f66348c7c4ffbfc5ac7cd4a4d4450c9d1c5ea8fdd8f4f9d38d1d0ba5b4ac9c53f1a754d3985dc483fe22e76f93a8bbe8ae29ef3b98136e7d2e
+    HEAD_REF develop
+    PATCHES
+        0001-set-linkage.patch
+        0002-pthread-flag.patch
+        0003-no-tests.patch
+        0004-fix-find-htscodecs.patch
+)
+
+set(FEATURE_OPTIONS "")
+
+macro(enable_feature feature switch)
+    if("${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")

ports/htslib/vcpkg.json

@@ -0,0 +1,32 @@
+{
+  "name": "htslib",
+  "version": "1.20",
+  "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"
+      ]
+    }
+  }
+}

versions/baseline.json

@@ -3468,6 +3468,14 @@
       "baseline": "1.10.0",
       "port-version": 1
     },
+    "htscodecs": {
+      "baseline": "1.6.0",
+      "port-version": 0
+    },
+    "htslib": {
+      "baseline": "1.20",
+      "port-version": 0
+    },
     "http-parser": {
       "baseline": "2.9.4",
       "port-version": 3

versions/h-/htscodecs.json

@@ -0,0 +1,9 @@
+{
+  "versions": [
+    {
+      "git-tree": "9475b0327f2fedd60e7c2d71351fed598c9ba3f9",
+      "version": "1.6.0",
+      "port-version": 0
+    }
+  ]
+}

versions/h-/htslib.json

@@ -0,0 +1,9 @@
+{
+  "versions": [
+    {
+      "git-tree": "94372bcc6471960499da89e7ca144bb90b43a235",
+      "version": "1.20",
+      "port-version": 0
+    }
+  ]
+}