git: a2fa05009fd2 - main - biology/minimap2: Update to 2.18

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=a2fa05009fd280fcf8e93f1062b554fdcca63c9a

commit a2fa05009fd280fcf8e93f1062b554fdcca63c9a
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-04-11 19:16:28 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-04-11 19:18:02 +0000

    biology/minimap2: Update to 2.18
    
    Numerous bug fixes and a few minor improvements
    
    Reported by:    portscout
---
 biology/minimap2/Makefile             | 2 +-
 biology/minimap2/distinfo             | 6 +++---
 biology/minimap2/files/patch-Makefile | 8 +++-----
 3 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile
index e8570bd99479..d99da2bcc4b5 100644
--- a/biology/minimap2/Makefile
+++ b/biology/minimap2/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		minimap2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.17
+DISTVERSION=		2.18
 CATEGORIES=		biology
 
 MAINTAINER=	jwb at FreeBSD.org
diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo
index aa8229da44d3..69632d44a87f 100644
--- a/biology/minimap2/distinfo
+++ b/biology/minimap2/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1557067380
-SHA256 (lh3-minimap2-v2.17_GH0.tar.gz) = 0a3eaa3ef3d9f9e41f48199cc4aac0508366ac644fc3e8fe05e3463acd23d20b
-SIZE (lh3-minimap2-v2.17_GH0.tar.gz) = 224006
+TIMESTAMP = 1618167822
+SHA256 (lh3-minimap2-v2.18_GH0.tar.gz) = efe75148342decd67e16f6a9ae14918ab9e1d67cadcfab5698b847f5b66f55e3
+SIZE (lh3-minimap2-v2.18_GH0.tar.gz) = 231187
diff --git a/biology/minimap2/files/patch-Makefile b/biology/minimap2/files/patch-Makefile
index f9008ea92a76..19bf99b1325d 100644
--- a/biology/minimap2/files/patch-Makefile
+++ b/biology/minimap2/files/patch-Makefile
@@ -1,10 +1,8 @@
---- Makefile.orig	2019-05-05 03:49:17 UTC
+--- Makefile.orig	2019-02-28 20:49:24 UTC
 +++ Makefile
-@@ -1,11 +1,21 @@
+@@ -1,11 +1,19 @@
 -CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
 -CPPFLAGS=	-DHAVE_KALLOC
-+# Patches using ?= and adding install target were rejected by developers
-+# https://github.com/lh3/minimap2/issues/388
 +CFLAGS?=	-g -Wall -O2
 +CFLAGS+=	-Wc++-compat #-Wextra
 +CPPFLAGS+=	-DHAVE_KALLOC
@@ -24,7 +22,7 @@
  ifeq ($(arm_neon),) # if arm_neon is not defined
  ifeq ($(sse2only),) # if sse2only is not defined
  	OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
-@@ -84,6 +94,15 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+@@ -84,6 +92,15 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
  		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
  
  # other non-file targets