git: 5ce41514802c - main - biology/htslib: Update to 1.17

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=5ce41514802cd442c01388c30a97e1fde16d836f

commit 5ce41514802cd442c01388c30a97e1fde16d836f
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-02-24 23:23:25 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-02-24 23:23:25 +0000

    biology/htslib: Update to 1.17
    
    Numerous enhancements and fixes
    
    Changes:    https://github.com/samtools/htslib/releases
    
    Reported by:    portscout
---
 biology/htslib/Makefile             |  2 +-
 biology/htslib/distinfo             |  6 +++---
 biology/htslib/files/patch-Makefile | 37 +++++++++----------------------------
 3 files changed, 13 insertions(+), 32 deletions(-)

diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
index 383f90e08114..9f85da45917a 100644
--- a/biology/htslib/Makefile
+++ b/biology/htslib/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	htslib
-DISTVERSION=	1.16
+DISTVERSION=	1.17
 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 88b848aeb2fb..24c398cacc3c 100644
--- a/biology/htslib/distinfo
+++ b/biology/htslib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1672094487
-SHA256 (htslib-1.16.tar.bz2) = 606b7c7aff73734cf033ecd156f40529fa5792f54524952a28938ca0890d7924
-SIZE (htslib-1.16.tar.bz2) = 4466776
+TIMESTAMP = 1677245487
+SHA256 (htslib-1.17.tar.bz2) = 763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f
+SIZE (htslib-1.17.tar.bz2) = 4619884
diff --git a/biology/htslib/files/patch-Makefile b/biology/htslib/files/patch-Makefile
index 7f91465d2ccd..eb6fb7f85901 100644
--- a/biology/htslib/files/patch-Makefile
+++ b/biology/htslib/files/patch-Makefile
@@ -1,33 +1,14 @@
---- Makefile.orig	2021-03-20 15:53:14 UTC
+--- Makefile.orig	2023-02-24 13:35:28 UTC
 +++ Makefile
-@@ -53,13 +53,14 @@ man5dir     = $(mandir)/man5
- man7dir     = $(mandir)/man7
- pkgconfigdir= $(prefix)/libdata/pkgconfig
- 
--MKDIR_P = mkdir -p
--INSTALL = install -p
--INSTALL_DATA    = $(INSTALL) -m 644
--INSTALL_DIR     = $(MKDIR_P) -m 755
--INSTALL_LIB     = $(INSTALL_DATA)
--INSTALL_MAN     = $(INSTALL_DATA)
+@@ -60,9 +60,9 @@ INSTALL = install -p
+ INSTALL_DATA    = $(INSTALL) -m 644
+ INSTALL_DIR     = $(MKDIR_P) -m 755
+ LIB_PERM        = 644
+-INSTALL_LIB     = $(INSTALL) -m $(LIB_PERM)
++INSTALL_LIB     = $(BSD_INSTALL_LIB)
+ INSTALL_MAN     = $(INSTALL_DATA)
 -INSTALL_PROGRAM = $(INSTALL)
-+# Use ports BSD_INSTALL_PROGRAM to strip if WITH_DEBUG is not set
-+MKDIR_P         = mkdir -p
-+INSTALL 	= install -p
-+INSTALL_DATA    = ${BSD_INSTALL_DATA}
-+INSTALL_DIR     = $(MKDIR_P)
-+INSTALL_LIB     = ${BSD_INSTALL_LIB}
-+INSTALL_MAN     = ${BSD_INSTALL_MAN}
-+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
++INSTALL_PROGRAM = $(BSD_INSTALL_PROGRAM)
  
  # Set by config.mk if plugins are enabled
  plugindir =
-@@ -102,7 +103,7 @@ 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)