Skip site navigation (1)Skip section navigation (2)
Date:      Fri, 29 Sep 2023 18:25:39 GMT
From:      "Jason W. Bacon" <jwb@FreeBSD.org>
To:        ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org
Subject:   git: f3576d9ad821 - main - biology/wfa2-lib: Update to 2.3.4
Message-ID:  <202309291825.38TIPd62067846@gitrepo.freebsd.org>

next in thread | raw e-mail | index | archive | help
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=f3576d9ad8210076b1f2e81f0bea81f48947f234

commit f3576d9ad8210076b1f2e81f0bea81f48947f234
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-09-29 18:24:07 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-09-29 18:24:07 +0000

    biology/wfa2-lib: Update to 2.3.4
    
    A few bug fixes
    Changes: https://github.com/smarco/WFA2-lib/releases
    
    Reported by:    portscout
---
 biology/wfa2-lib/Makefile                                     |  3 +--
 biology/wfa2-lib/distinfo                                     |  6 +++---
 biology/wfa2-lib/files/patch-CMakeLists.txt                   |  2 +-
 .../files/patch-wavefront_wavefront__extend__kernels.c        | 11 +++++++++++
 biology/wfa2-lib/pkg-plist                                    |  9 ++++++++-
 5 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/biology/wfa2-lib/Makefile b/biology/wfa2-lib/Makefile
index 2300f379ec6f..a8a95a8229d4 100644
--- a/biology/wfa2-lib/Makefile
+++ b/biology/wfa2-lib/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		wfa2-lib
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.3.2
-PORTREVISION=		1
+DISTVERSION=		2.3.4
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/wfa2-lib/distinfo b/biology/wfa2-lib/distinfo
index 09a5d3555324..ab50e1352a95 100644
--- a/biology/wfa2-lib/distinfo
+++ b/biology/wfa2-lib/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1675088499
-SHA256 (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 310e3886506ab57d04205cdf5fed3ef31969ce39e9c6d341fd5c8a0d4aa0830b
-SIZE (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 4150874
+TIMESTAMP = 1695995337
+SHA256 (smarco-WFA2-lib-v2.3.4_GH0.tar.gz) = 3a02d19b45c7efcdcabdd956421b1e449e771fca0b0f072e02d7aa65ebb29f23
+SIZE (smarco-WFA2-lib-v2.3.4_GH0.tar.gz) = 4224505
diff --git a/biology/wfa2-lib/files/patch-CMakeLists.txt b/biology/wfa2-lib/files/patch-CMakeLists.txt
index 8b71ad656f0a..5be0031f15f4 100644
--- a/biology/wfa2-lib/files/patch-CMakeLists.txt
+++ b/biology/wfa2-lib/files/patch-CMakeLists.txt
@@ -1,4 +1,4 @@
---- CMakeLists.txt.orig	2023-01-31 15:02:27 UTC
+--- CMakeLists.txt.orig	2023-09-29 13:47:52 UTC
 +++ CMakeLists.txt
 @@ -55,7 +55,7 @@ if(NOT CMAKE_BUILD_TYPE)
  endif()
diff --git a/biology/wfa2-lib/files/patch-wavefront_wavefront__extend__kernels.c b/biology/wfa2-lib/files/patch-wavefront_wavefront__extend__kernels.c
new file mode 100644
index 000000000000..c46271b7a21e
--- /dev/null
+++ b/biology/wfa2-lib/files/patch-wavefront_wavefront__extend__kernels.c
@@ -0,0 +1,11 @@
+--- wavefront/wavefront_extend_kernels.c.orig	2023-09-29 17:25:17 UTC
++++ wavefront/wavefront_extend_kernels.c
+@@ -29,7 +29,7 @@
+  * DESCRIPTION: WFA module for the "extension" of exact matches
+  */
+ 
+-#include <endian.h>
++#include <sys/endian.h>
+ 
+ #include "wavefront_extend_kernels.h"
+ #include "wavefront_termination.h"
diff --git a/biology/wfa2-lib/pkg-plist b/biology/wfa2-lib/pkg-plist
index 235ff54015ca..2fa4ac482adc 100644
--- a/biology/wfa2-lib/pkg-plist
+++ b/biology/wfa2-lib/pkg-plist
@@ -3,6 +3,7 @@ include/wfa2lib/alignment/affine_penalties.h
 include/wfa2lib/alignment/cigar.h
 include/wfa2lib/alignment/linear_penalties.h
 include/wfa2lib/alignment/score_matrix.h
+include/wfa2lib/bindings/cpp/WFAligner.hpp
 include/wfa2lib/system/mm_allocator.h
 include/wfa2lib/system/mm_stack.h
 include/wfa2lib/system/profiler_counter.h
@@ -12,7 +13,6 @@ include/wfa2lib/utils/commons.h
 include/wfa2lib/utils/dna_text.h
 include/wfa2lib/utils/heatmap.h
 include/wfa2lib/utils/sequence_buffer.h
-include/wfa2lib/utils/string_padded.h
 include/wfa2lib/utils/vector.h
 include/wfa2lib/wavefront/wavefront.h
 include/wfa2lib/wavefront/wavefront_align.h
@@ -32,15 +32,22 @@ include/wfa2lib/wavefront/wavefront_compute_linear.h
 include/wfa2lib/wavefront/wavefront_debug.h
 include/wfa2lib/wavefront/wavefront_display.h
 include/wfa2lib/wavefront/wavefront_extend.h
+include/wfa2lib/wavefront/wavefront_extend_kernels.h
+include/wfa2lib/wavefront/wavefront_extend_kernels_avx.h
 include/wfa2lib/wavefront/wavefront_heuristic.h
 include/wfa2lib/wavefront/wavefront_offset.h
 include/wfa2lib/wavefront/wavefront_pcigar.h
 include/wfa2lib/wavefront/wavefront_penalties.h
 include/wfa2lib/wavefront/wavefront_plot.h
+include/wfa2lib/wavefront/wavefront_sequences.h
 include/wfa2lib/wavefront/wavefront_slab.h
+include/wfa2lib/wavefront/wavefront_termination.h
 include/wfa2lib/wavefront/wavefront_unialign.h
 include/wfa2lib/wavefront/wfa.h
 include/wfa2lib/wavefront/wfa.hpp
 lib/libwfa2.a
 lib/libwfa2.so
 lib/libwfa2.so.0
+lib/libwfa2cpp.a
+lib/libwfa2cpp.so
+lib/libwfa2cpp.so.0



Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202309291825.38TIPd62067846>