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[htslib, htscodecs] Update to latest versions. (#41644)

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Theodore Tsirpanis 2024-10-19 02:52:42 +03:00 committed by GitHub
parent ce2e65766e
commit 21b088936b
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10 changed files with 33 additions and 11 deletions
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2
ports/htscodecs/portfile.cmake
View File

@ -2,7 +2,7 @@ vcpkg_from_github(
OUT_SOURCE_PATH SOURCE_PATH
REPO samtools/htscodecs
REF "v${VERSION}"
SHA512 7533570b8b1cad0b9ed118170e5a9ff34fdde40b090f4ba3756f7899e2cd7230f8172425ecf6bd7b83b0b0b1a2a24f3d21795db7f0bc2c3add0a55342b970d1a
SHA512 5e3e1f916cb14fe7e1292f3a07e9d9704b11be38014db5884b334235c25dbe61dffecf3f12c448a7a13f65c6d19dbc7cc5c77ba0861b31a0375d71030dd02480
HEAD_REF master
PATCHES
0001-no-tests.patch # https://github.com/samtools/htscodecs/pull/120

2
ports/htscodecs/vcpkg.json
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@ -1,6 +1,6 @@
{
"name": "htscodecs",
"version": "1.6.0",
"version": "1.6.1",
"description": "Custom compression for CRAM and others.",
"homepage": "https://github.com/samtools/htscodecs",
"license": "MIT",

2
ports/htslib/0002-pthread-flag.patch
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@ -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)
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)

8
ports/htslib/0003-no-tests.patch
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@ -6,8 +6,8 @@ index fb4f527..751df4b 100644
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: lib-static lib-shared $(BUILT_PROGRAMS) plugins \
- $(BUILT_TEST_PROGRAMS) htslib_static.mk htslib-uninstalled.pc
+ htslib_static.mk htslib-uninstalled.pc
ALL_CPPFLAGS = -I. $(CPPFLAGS)
# Report compiler and version

11
ports/htslib/0005-remove-duplicate-lhts.patch Normal file
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@ -0,0 +1,11 @@
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@

3
ports/htslib/portfile.cmake
View File

@ -2,13 +2,14 @@ vcpkg_from_github(
OUT_SOURCE_PATH SOURCE_PATH
REPO samtools/htslib
REF "${VERSION}"
SHA512 b9de3769db6153f66348c7c4ffbfc5ac7cd4a4d4450c9d1c5ea8fdd8f4f9d38d1d0ba5b4ac9c53f1a754d3985dc483fe22e76f93a8bbe8ae29ef3b98136e7d2e
SHA512 6df1a493ac9f13cae5a510537bdf83aa9635a79efe635b8a5a5cbd89345c75c9a42e686c4f0497761ddfad3b86a9814ed35ba2ac340d0f1c7b5e2e186b152875
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
)
set(FEATURE_OPTIONS "")

2
ports/htslib/vcpkg.json
View File

@ -1,6 +1,6 @@
{
"name": "htslib",
"version": "1.20",
"version": "1.21",
"description": "C library for high-throughput sequencing data formats",
"homepage": "https://github.com/samtools/htslib",
"license": "MIT",

4
versions/baseline.json
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@ -3505,11 +3505,11 @@
"port-version": 1
},
"htscodecs": {
"baseline": "1.6.0",
"baseline": "1.6.1",
"port-version": 0
},
"htslib": {
"baseline": "1.20",
"baseline": "1.21",
"port-version": 0
},
"http-parser": {

5
versions/h-/htscodecs.json
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@ -1,5 +1,10 @@
{
"versions": [
{
"git-tree": "a7eaba66bb4d3bf35e1a6b9b70e91edccaccf071",
"version": "1.6.1",
"port-version": 0
},
{
"git-tree": "9475b0327f2fedd60e7c2d71351fed598c9ba3f9",
"version": "1.6.0",

5
versions/h-/htslib.json
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@ -1,5 +1,10 @@
{
"versions": [
{
"git-tree": "76f12c76144128b5c812e8c80957daa446b8b29e",
"version": "1.21",
"port-version": 0
},
{
"git-tree": "94372bcc6471960499da89e7ca144bb90b43a235",
"version": "1.20",