git: 027b959425c8 - main - biology/minimap2: Update to 2.30

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Mon, 16 Jun 2025 13:10:20 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=027b959425c8f93248d65e5a4407d23ff021ace3

commit 027b959425c8f93248d65e5a4407d23ff021ace3
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-06-16 13:08:50 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-06-16 13:08:50 +0000

    biology/minimap2: Update to 2.30
    
    Deprecate several subcommands, replaced by minigff
    Changes: https://github.com/lh3/minimap2/releases
    
    Reported by:    portscout
---
 biology/minimap2/Makefile       |  2 +-
 biology/minimap2/distinfo       |  6 +++---
 biology/minimap2/patch.minimap2 | 31 +++++++++++++++++++++++++++++++
 biology/minimap2/pkg-plist      |  3 +++
 4 files changed, 38 insertions(+), 4 deletions(-)

diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile
index eb65d48578c5..dd10b6869afe 100644
--- a/biology/minimap2/Makefile
+++ b/biology/minimap2/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		minimap2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.29
+DISTVERSION=		2.30
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo
index fac01c43c7f5..f7c616549712 100644
--- a/biology/minimap2/distinfo
+++ b/biology/minimap2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1745154104
-SHA256 (lh3-minimap2-v2.29_GH0.tar.gz) = 008d5e9848b918e4eb09d054aa3d6c272d50e92b8fc8537abf5081a507019718
-SIZE (lh3-minimap2-v2.29_GH0.tar.gz) = 269107
+TIMESTAMP = 1750076274
+SHA256 (lh3-minimap2-v2.30_GH0.tar.gz) = 4e5cd621be2b2685c5c88d9b9b169c7e036ab9fff2f3afe1a1d4091ae3176380
+SIZE (lh3-minimap2-v2.30_GH0.tar.gz) = 269912
diff --git a/biology/minimap2/patch.minimap2 b/biology/minimap2/patch.minimap2
new file mode 100644
index 000000000000..5b7080cb43d3
--- /dev/null
+++ b/biology/minimap2/patch.minimap2
@@ -0,0 +1,31 @@
+diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/minimap2/Makefile /usr/ports/wip/minimap2/Makefile
+--- /usr/ports/biology/minimap2/Makefile	2025-04-20 08:14:09.261908000 -0500
++++ /usr/ports/wip/minimap2/Makefile	2025-06-16 08:07:58.592212000 -0500
+@@ -1,6 +1,6 @@
+ PORTNAME=		minimap2
+ DISTVERSIONPREFIX=	v
+-DISTVERSION=		2.29
++DISTVERSION=		2.30
+ CATEGORIES=		biology
+ 
+ MAINTAINER=	jwb@FreeBSD.org
+diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/minimap2/distinfo /usr/ports/wip/minimap2/distinfo
+--- /usr/ports/biology/minimap2/distinfo	2025-04-20 08:13:48.648889000 -0500
++++ /usr/ports/wip/minimap2/distinfo	2025-06-16 08:07:57.620437000 -0500
+@@ -1,3 +1,3 @@
+-TIMESTAMP = 1745154104
+-SHA256 (lh3-minimap2-v2.29_GH0.tar.gz) = 008d5e9848b918e4eb09d054aa3d6c272d50e92b8fc8537abf5081a507019718
+-SIZE (lh3-minimap2-v2.29_GH0.tar.gz) = 269107
++TIMESTAMP = 1750076274
++SHA256 (lh3-minimap2-v2.30_GH0.tar.gz) = 4e5cd621be2b2685c5c88d9b9b169c7e036ab9fff2f3afe1a1d4091ae3176380
++SIZE (lh3-minimap2-v2.30_GH0.tar.gz) = 269912
+diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/minimap2/pkg-plist /usr/ports/wip/minimap2/pkg-plist
+--- /usr/ports/biology/minimap2/pkg-plist	2024-04-17 17:51:07.042256000 -0500
++++ /usr/ports/wip/minimap2/pkg-plist	2025-06-16 08:07:57.620515000 -0500
+@@ -8,3 +8,6 @@
+ %%DATADIR%%/test/q2.fa
+ %%DATADIR%%/test/t-inv.fa
+ %%DATADIR%%/test/t2.fa
++%%DATADIR%%/test/x3s-aln.txt
++%%DATADIR%%/test/x3s-qry.fa
++%%DATADIR%%/test/x3s-ref.fa
diff --git a/biology/minimap2/pkg-plist b/biology/minimap2/pkg-plist
index 742d1eb1b3f7..9e386df64f48 100644
--- a/biology/minimap2/pkg-plist
+++ b/biology/minimap2/pkg-plist
@@ -8,3 +8,6 @@ share/man/man1/minimap2.1.gz
 %%DATADIR%%/test/q2.fa
 %%DATADIR%%/test/t-inv.fa
 %%DATADIR%%/test/t2.fa
+%%DATADIR%%/test/x3s-aln.txt
+%%DATADIR%%/test/x3s-qry.fa
+%%DATADIR%%/test/x3s-ref.fa