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biology/htslib: Update to 1.21

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Numerous bug fixes and enhancements since 1.17
Changes:        https://github.com/samtools/htslib/releases

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2024-10-09 17:06:24 -05:00
parent 83ec241c54
commit aafe5d31c5
5 changed files with 14 additions and 13 deletions
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5
biology/htslib/Makefile
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@ -1,6 +1,5 @@
PORTNAME= htslib PORTNAME= htslib
DISTVERSION= 1.17 DISTVERSION= 1.21
PORTREVISION= 1
CATEGORIES= biology devel CATEGORIES= biology devel
# Github generated distfiles are incomplete, so use custom tarball # Github generated distfiles are incomplete, so use custom tarball
MASTER_SITES= https://github.com/samtools/htslib/releases/download/${DISTVERSION}/ MASTER_SITES= https://github.com/samtools/htslib/releases/download/${DISTVERSION}/
@ -24,7 +23,7 @@ GNU_CONFIGURE= yes
GNU_CONFIGURE_MANPREFIX=${PREFIX}/share GNU_CONFIGURE_MANPREFIX=${PREFIX}/share
MAKE_ARGS_armv6= HTS_HAVE_NEON= MAKE_ARGS_armv6= HTS_HAVE_NEON=
MAKE_ARGS_armv7= HTS_HAVE_NEON= MAKE_ARGS_armv7= HTS_HAVE_NEON=
MAKE_ARGS= $(MAKE_ARGS_$(ARCH)) MAKE_ARGS= ${MAKE_ARGS_${ARCH}}
PATHFIX_MAKEFILEIN= Makefile PATHFIX_MAKEFILEIN= Makefile
SHEBANG_FILES= test/*.pl SHEBANG_FILES= test/*.pl

6
biology/htslib/distinfo
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@ -1,3 +1,3 @@
TIMESTAMP = 1677245487 TIMESTAMP = 1727437235
SHA256 (htslib-1.17.tar.bz2) = 763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f SHA256 (htslib-1.21.tar.bz2) = 84b510e735f4963641f26fd88c8abdee81ff4cb62168310ae716636aac0f1823
SIZE (htslib-1.17.tar.bz2) = 4619884 SIZE (htslib-1.21.tar.bz2) = 4781943

6
biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c
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@ -1,11 +1,11 @@
--- htscodecs/htscodecs/rANS_static32x16pr_neon.c.orig 2023-04-17 21:11:08 UTC --- htscodecs/htscodecs/rANS_static32x16pr_neon.c.orig 2024-10-09 21:43:35 UTC
+++ htscodecs/htscodecs/rANS_static32x16pr_neon.c +++ htscodecs/htscodecs/rANS_static32x16pr_neon.c
@@ -32,7 +32,7 @@ @@ -32,7 +32,7 @@
*/ */
#include "config.h" #include "config.h"
-#ifdef __ARM_NEON -#if defined(__ARM_NEON) && defined(__aarch64__)
+#if defined(__ARM_NEON) && defined(__aarch64__) +#if defined(__ARM_NEON)
#include <arm_neon.h> #include <arm_neon.h>
#include <limits.h> #include <limits.h>

8
biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c
View File

@ -1,11 +1,11 @@
--- htscodecs/htscodecs/rANS_static4x16pr.c.orig 2023-04-17 21:13:50 UTC --- htscodecs/htscodecs/rANS_static4x16pr.c.orig 2024-10-09 21:44:38 UTC
+++ htscodecs/htscodecs/rANS_static4x16pr.c +++ htscodecs/htscodecs/rANS_static4x16pr.c
@@ -1006,7 +1006,7 @@ unsigned char *(*rans_dec_func(int do_simd, int order) @@ -1030,7 +1030,7 @@ unsigned char *(*rans_dec_func(int do_simd, int order)
} }
} }
-#elif defined(__ARM_NEON) -#elif defined(__ARM_NEON) && defined(__aarch64__)
+#elif defined(__ARM_NEON) && defined(__aarch64__) +#elif defined(__ARM_NEON)
#if defined(__linux__) || defined(__FreeBSD__) #if defined(__linux__) || defined(__FreeBSD__)
#include <sys/auxv.h> #include <sys/auxv.h>

2
biology/htslib/pkg-plist
View File

@ -1,3 +1,4 @@
bin/annot-tsv
bin/bgzip bin/bgzip
bin/htsfile bin/htsfile
bin/tabix bin/tabix
@ -34,6 +35,7 @@ lib/libhts.so
lib/libhts.so.%%PORTVERSION%% lib/libhts.so.%%PORTVERSION%%
lib/libhts.so.3 lib/libhts.so.3
libdata/pkgconfig/htslib.pc libdata/pkgconfig/htslib.pc
share/man/man1/annot-tsv.1.gz
share/man/man1/bgzip.1.gz share/man/man1/bgzip.1.gz
share/man/man1/htsfile.1.gz share/man/man1/htsfile.1.gz
share/man/man1/tabix.1.gz share/man/man1/tabix.1.gz