git: f3576d9ad821 - main - biology/wfa2-lib: Update to 2.3.4
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Date: Fri, 29 Sep 2023 18:25:39 UTC
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