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Port details
wfa2-lib Exact gap-affine algorithm using homology to accelerate alignment
2.3.5 biology on this many watch lists=2 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.3.5Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2023-01-30 19:12:07
Last Update: 2024-08-04 12:00:47
Commit Hash: a732098
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
License: MIT
WWW:
https://github.com/smarco/WFA2-lib
Description:
The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. Unlike traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns+s^2), proportional to the sequence length n and the alignment score s, using O(s^2) memory (or O(s) using the ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple computational patterns that the modern compilers can automatically vectorize for different architectures without adapting the code.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (60 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/wfa2-lib-2.3.5/catalog.mk
  3. /usr/local/share/licenses/wfa2-lib-2.3.5/LICENSE
  4. /usr/local/share/licenses/wfa2-lib-2.3.5/MIT
  5. include/wfa2lib/alignment/affine2p_penalties.h
  6. include/wfa2lib/alignment/affine_penalties.h
  7. include/wfa2lib/alignment/cigar.h
  8. include/wfa2lib/alignment/linear_penalties.h
  9. include/wfa2lib/alignment/score_matrix.h
  10. include/wfa2lib/bindings/cpp/WFAligner.hpp
  11. include/wfa2lib/system/mm_allocator.h
  12. include/wfa2lib/system/mm_stack.h
  13. include/wfa2lib/system/profiler_counter.h
  14. include/wfa2lib/system/profiler_timer.h
  15. include/wfa2lib/utils/bitmap.h
  16. include/wfa2lib/utils/commons.h
  17. include/wfa2lib/utils/dna_text.h
  18. include/wfa2lib/utils/heatmap.h
  19. include/wfa2lib/utils/sequence_buffer.h
  20. include/wfa2lib/utils/vector.h
  21. include/wfa2lib/wavefront/wavefront.h
  22. include/wfa2lib/wavefront/wavefront_align.h
  23. include/wfa2lib/wavefront/wavefront_aligner.h
  24. include/wfa2lib/wavefront/wavefront_attributes.h
  25. include/wfa2lib/wavefront/wavefront_backtrace.h
  26. include/wfa2lib/wavefront/wavefront_backtrace_buffer.h
  27. include/wfa2lib/wavefront/wavefront_backtrace_offload.h
  28. include/wfa2lib/wavefront/wavefront_bialign.h
  29. include/wfa2lib/wavefront/wavefront_bialigner.h
  30. include/wfa2lib/wavefront/wavefront_components.h
  31. include/wfa2lib/wavefront/wavefront_compute.h
  32. include/wfa2lib/wavefront/wavefront_compute_affine.h
  33. include/wfa2lib/wavefront/wavefront_compute_affine2p.h
  34. include/wfa2lib/wavefront/wavefront_compute_edit.h
  35. include/wfa2lib/wavefront/wavefront_compute_linear.h
  36. include/wfa2lib/wavefront/wavefront_debug.h
  37. include/wfa2lib/wavefront/wavefront_display.h
  38. include/wfa2lib/wavefront/wavefront_extend.h
  39. include/wfa2lib/wavefront/wavefront_extend_kernels.h
  40. include/wfa2lib/wavefront/wavefront_extend_kernels_avx.h
  41. include/wfa2lib/wavefront/wavefront_heuristic.h
  42. include/wfa2lib/wavefront/wavefront_offset.h
  43. include/wfa2lib/wavefront/wavefront_pcigar.h
  44. include/wfa2lib/wavefront/wavefront_penalties.h
  45. include/wfa2lib/wavefront/wavefront_plot.h
  46. include/wfa2lib/wavefront/wavefront_sequences.h
  47. include/wfa2lib/wavefront/wavefront_slab.h
  48. include/wfa2lib/wavefront/wavefront_termination.h
  49. include/wfa2lib/wavefront/wavefront_unialign.h
  50. include/wfa2lib/wavefront/wfa.h
  51. include/wfa2lib/wavefront/wfa.hpp
  52. lib/libwfa2.a
  53. lib/libwfa2.so
  54. lib/libwfa2.so.0
  55. lib/libwfa2cpp.a
  56. lib/libwfa2cpp.so
  57. lib/libwfa2cpp.so.0
  58. @owner
  59. @group
  60. @mode
Collapse this list.
Dependency lines:
  • wfa2-lib>0:biology/wfa2-lib
To install the port:
cd /usr/ports/biology/wfa2-lib/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/wfa2-lib
  • pkg install wfa2-lib
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: wfa2-lib
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1713703314 SHA256 (smarco-WFA2-lib-v2.3.5_GH0.tar.gz) = 2609d5f267f4dd91dce1776385b5a24a2f1aa625ac844ce0c3571c69178afe6e SIZE (smarco-WFA2-lib-v2.3.5_GH0.tar.gz) = 4225016
Packages (timestamps in pop-ups are UTC):
wfa2-lib
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.3.52.3.5-2.3.52.3.5---
FreeBSD:13:quarterly2.3.52.3.52.3.2_12.3.52.3.52.3.42.3.42.3.4
FreeBSD:14:latest2.3.52.3.5-2.3.52.3.52.3.2_1-2.3.2_1
FreeBSD:14:quarterly2.3.52.3.5-2.3.52.3.52.3.42.3.42.3.4
FreeBSD:15:latest2.3.52.3.5n/a2.3.5n/a2.3.42.3.42.3.4
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake-core
  2. ninja : devel/ninja
  3. pkgconf>=1.3.0_1 : devel/pkgconf
This port is required by:
for Libraries
  1. biology/vcflib
Configuration Options:
No options to configure
Options name:
biology_wfa2-lib
USES:
cmake pkgconfig
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/smarco/WFA2-lib/tar.gz/v2.3.5?dummy=/
Collapse this list.

Number of commits found: 6

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.3.5
04 Aug 2024 12:00:47
commit hash: a7320981d5d4530534f241001f2e91f687dd5796commit hash: a7320981d5d4530534f241001f2e91f687dd5796commit hash: a7320981d5d4530534f241001f2e91f687dd5796commit hash: a7320981d5d4530534f241001f2e91f687dd5796 files touched by this commit		 Piotr Kubaj (pkubaj) search for other commits by this committer 
biology/wfa2-lib: fix build without libomp

/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark/align_benchmark.c:32:10:
fatal error: 'omp.h' file not found
   32 | #include <omp.h>
      |          ^~~~~~~
1 error generated.
2.3.5
22 Apr 2024 12:42:04
commit hash: 1de14dfc3b4cc9a6fd04afd9a5e1dccb569993e1commit hash: 1de14dfc3b4cc9a6fd04afd9a5e1dccb569993e1commit hash: 1de14dfc3b4cc9a6fd04afd9a5e1dccb569993e1commit hash: 1de14dfc3b4cc9a6fd04afd9a5e1dccb569993e1 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/wfa2-lib: Update to 2.3.5

A few bug fixes.
Changes: https://github.com/smarco/WFA2-lib/releases

Reported by:    portscout
2.3.4
29 Sep 2023 18:24:07
commit hash: f3576d9ad8210076b1f2e81f0bea81f48947f234commit hash: f3576d9ad8210076b1f2e81f0bea81f48947f234commit hash: f3576d9ad8210076b1f2e81f0bea81f48947f234commit hash: f3576d9ad8210076b1f2e81f0bea81f48947f234 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/wfa2-lib: Update to 2.3.4

A few bug fixes
Changes: https://github.com/smarco/WFA2-lib/releases

Reported by:    portscout
2.3.2_1
30 Mar 2023 23:59:51
commit hash: 56932296b7bc5c29380a4c433c5a9250fb6b4fb5commit hash: 56932296b7bc5c29380a4c433c5a9250fb6b4fb5commit hash: 56932296b7bc5c29380a4c433c5a9250fb6b4fb5commit hash: 56932296b7bc5c29380a4c433c5a9250fb6b4fb5 files touched by this commit		 Muhammad Moinur Rahman (bofh) search for other commits by this committer 
*/*: Sunset 12.3-RELEASE from ports tree

- Mk/bsd.port.mk: mark FreeBSD 12.3 as unsupported.
- Mk/Uses/cabal.mk: Remove the text-2 workaround for 12.3-RELEASE
- biology/wfa2-lib: remove obsolete patch
- databases/mongodb60: remove IGNORE for EOL FreeBSD 12.3
- devel/concurrencpp: remove workaround for EOL FreeBSD 12.3
- devel/electron22: remove IGNORE for EOL FreeBSD 12.3
- devel/malloy: this should build fine on 12.4-RELEASE
- devel/qcoro: remove BROKEN for EOL FreeBSD 12.3
- devel/root: remove workaround for EOL FreeBSD 12.3
- editors/imhex: remove IGNORE for EOL FreeBSD 12.3
- emulators/ppsspp: remove workaround for EOL FreeBSD 12.3
- emulators/rpcs3: remove workaround for EOL FreeBSD 12.3
- emulators/yuzu: remove workaround for EOL 12.3-RELEASE
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.3.2_1
31 Jan 2023 15:17:52
commit hash: eb340a643efc7a5d40858fb9abc059bb9face05ccommit hash: eb340a643efc7a5d40858fb9abc059bb9face05ccommit hash: eb340a643efc7a5d40858fb9abc059bb9face05ccommit hash: eb340a643efc7a5d40858fb9abc059bb9face05c files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/wfa2-lib: Unbreak build on aarch64, probably others

Patch out hard-coded -march=native, not supported by clang aarch64

Reported by:    pkg-fallout
2.3.2
30 Jan 2023 19:09:02
commit hash: 595d0dabcfdc4e4a2eefbfff154f7c2ab04488becommit hash: 595d0dabcfdc4e4a2eefbfff154f7c2ab04488becommit hash: 595d0dabcfdc4e4a2eefbfff154f7c2ab04488becommit hash: 595d0dabcfdc4e4a2eefbfff154f7c2ab04488be files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/wfa2-lib: Exact gap-affine algorithm using homology

The wavefront alignment (WFA) algorithm is an exact gap-affine
algorithm that takes advantage of homologous regions between the
sequences to accelerate the alignment process.  Unlike traditional
dynamic programming algorithms that run in quadratic time, the WFA runs
in time O(ns+s^2), proportional to the sequence length n and the
alignment score s, using O(s^2) memory (or O(s) using the
ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple
computational patterns that the modern compilers can automatically
vectorize for different architectures without adapting the code.

Number of commits found: 6
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