git: b44b3ccb00d6 - main - biology/htslib: Update to 1.24
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Date: Sat, 11 Jul 2026 19:33:23 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=b44b3ccb00d6f4d1648fcc2355a53d158d295887
commit b44b3ccb00d6f4d1648fcc2355a53d158d295887
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-07-11 19:21:04 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-07-11 19:21:04 +0000
biology/htslib: Update to 1.24
Numerous fixes and enhancements
Changes: https://github.com/samtools/htslib/releases
Reported by: portscout
---
biology/htslib/Makefile | 2 +-
biology/htslib/distinfo | 6 +++---
.../patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c | 11 +++++++++++
.../files/patch-htscodecs_htscodecs_rANS__static4x16pr.c | 11 +++++++++++
biology/htslib/pkg-plist | 1 +
5 files changed, 27 insertions(+), 4 deletions(-)
diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
index aa4f02a37d15..e600db8cec64 100644
--- a/biology/htslib/Makefile
+++ b/biology/htslib/Makefile
@@ -1,5 +1,5 @@
PORTNAME= htslib
-DISTVERSION= 1.23.1
+DISTVERSION= 1.24
CATEGORIES= biology devel
# Github generated distfiles are incomplete, so use custom tarball
MASTER_SITES= https://github.com/samtools/htslib/releases/download/${DISTVERSION}/
diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo
index 257fe618a524..388227740105 100644
--- a/biology/htslib/distinfo
+++ b/biology/htslib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1774783712
-SHA256 (htslib-1.23.1.tar.bz2) = f8a3f36effeec38f043c53ab1f2d9ed45064f14205c5ef8e3c815763b90803c4
-SIZE (htslib-1.23.1.tar.bz2) = 4987046
+TIMESTAMP = 1783681751
+SHA256 (htslib-1.24.tar.bz2) = 28a8de191381c7a97a35675ceac76fa1ea95e7b678d6a2e9d600a7874e4077de
+SIZE (htslib-1.24.tar.bz2) = 5004265
diff --git a/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c
new file mode 100644
index 000000000000..434edf03f411
--- /dev/null
+++ b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c
@@ -0,0 +1,11 @@
+--- htscodecs/htscodecs/rANS_static32x16pr_neon.c.orig 2024-10-09 21:43:35 UTC
++++ htscodecs/htscodecs/rANS_static32x16pr_neon.c
+@@ -32,7 +32,7 @@
+ */
+
+ #include "config.h"
+-#if defined(__ARM_NEON) && defined(__aarch64__)
++#if defined(__ARM_NEON)
+ #include <arm_neon.h>
+
+ #include <limits.h>
diff --git a/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c
new file mode 100644
index 000000000000..3eaebe7ae36d
--- /dev/null
+++ b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c
@@ -0,0 +1,11 @@
+--- htscodecs/htscodecs/rANS_static4x16pr.c.orig 2024-10-09 21:44:38 UTC
++++ htscodecs/htscodecs/rANS_static4x16pr.c
+@@ -1030,7 +1030,7 @@ unsigned char *(*rans_dec_func(int do_simd, int order)
+ }
+ }
+
+-#elif defined(__ARM_NEON) && defined(__aarch64__)
++#elif defined(__ARM_NEON)
+
+ #if defined(__linux__) || defined(__FreeBSD__)
+ #include <sys/auxv.h>
diff --git a/biology/htslib/pkg-plist b/biology/htslib/pkg-plist
index 1825cfff6daf..1b33a6a4a67f 100644
--- a/biology/htslib/pkg-plist
+++ b/biology/htslib/pkg-plist
@@ -8,6 +8,7 @@ include/htslib/cram.h
include/htslib/faidx.h
include/htslib/hfile.h
include/htslib/hts.h
+include/htslib/hts_alloc.h
include/htslib/hts_defs.h
include/htslib/hts_endian.h
include/htslib/hts_expr.h