git: 8efa6a228307 - main - biology/minimap2: Update to 2.28

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=8efa6a2283076e4e556d7796161c44b90f5b3aa8

commit 8efa6a2283076e4e556d7796161c44b90f5b3aa8
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2024-04-10 12:28:02 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2024-04-10 12:28:02 +0000

    biology/minimap2: Update to 2.28
    
    Fix --MD flag
    Add experimental lr:hqae
    Changes: https://github.com/lh3/minimap2/releases
    
    Reported by:    portscout
---
 biology/minimap2/Makefile                   | 3 +--
 biology/minimap2/distinfo                   | 6 +++---
 biology/minimap2/files/patch-Makefile.simde | 6 +++---
 biology/minimap2/pkg-plist                  | 2 +-
 4 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile
index df9552ac6ca0..2539d53f0969 100644
--- a/biology/minimap2/Makefile
+++ b/biology/minimap2/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		minimap2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.27
-PORTREVISION=		1
+DISTVERSION=		2.28
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo
index 5a1bf73dfa7d..24b9f3d5dc0c 100644
--- a/biology/minimap2/distinfo
+++ b/biology/minimap2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1710332275
-SHA256 (lh3-minimap2-v2.27_GH0.tar.gz) = ca9ceb07e3b388858ebc2d7d91a6c74e996659402d16aa759ecedd63588b1ef7
-SIZE (lh3-minimap2-v2.27_GH0.tar.gz) = 259736
+TIMESTAMP = 1712360724
+SHA256 (lh3-minimap2-v2.28_GH0.tar.gz) = 5ea6683b4184b5c49f6dbaef2bc5b66155e405888a0790d1b21fd3c93e474278
+SIZE (lh3-minimap2-v2.28_GH0.tar.gz) = 260341
diff --git a/biology/minimap2/files/patch-Makefile.simde b/biology/minimap2/files/patch-Makefile.simde
index aac7981c6b10..5d5e0ccf482c 100644
--- a/biology/minimap2/files/patch-Makefile.simde
+++ b/biology/minimap2/files/patch-Makefile.simde
@@ -1,4 +1,4 @@
---- Makefile.simde.orig	2024-03-12 17:20:07 UTC
+--- Makefile.simde.orig	2021-11-18 22:11:48 UTC
 +++ Makefile.simde
 @@ -1,13 +1,26 @@
 -CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
@@ -21,7 +21,7 @@
  LIBS=		-lm -lz -lpthread
  
 +PREFIX?=	/usr/local
-+MAN1DIR?=	${PREFIX}/share/man/man1
++MAN1DIR?=	${PREFIX}/man/man1
 +DATADIR?=	${PREFIX}/share/minimap2
  
 +MKDIR?=		mkdir
@@ -32,7 +32,7 @@
  ifneq ($(arm_neon),) # if arm_neon is defined
  ifeq ($(aarch64),)   #if aarch64 is not defined
  	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
-@@ -26,7 +39,7 @@ endif
+@@ -26,7 +39,7 @@ ifneq ($(tsan),)
  	LIBS+=-fsanitize=thread
  endif
  
diff --git a/biology/minimap2/pkg-plist b/biology/minimap2/pkg-plist
index 742d1eb1b3f7..1d11d4c99c2f 100644
--- a/biology/minimap2/pkg-plist
+++ b/biology/minimap2/pkg-plist
@@ -1,7 +1,7 @@
 bin/minimap2
 bin/minimap2-lite
 bin/sdust
-share/man/man1/minimap2.1.gz
+man/man1/minimap2.1.gz
 %%DATADIR%%/test/MT-human.fa
 %%DATADIR%%/test/MT-orang.fa
 %%DATADIR%%/test/q-inv.fa