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Port details on branch 2022Q2
wfa2-lib Exact gap-affine algorithm using homology to accelerate alignment
2.3.4 biology on this many watch lists=0 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 2.3.4Version 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: 2023-09-29 18:24:07
Commit Hash: f3576d9
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-2.3.4/catalog.mk
  3. /usr/local/share/licenses/wfa2-lib-2.3.4/LICENSE
  4. /usr/local/share/licenses/wfa2-lib-2.3.4/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 = 1695995337 SHA256 (smarco-WFA2-lib-v2.3.4_GH0.tar.gz) = 3a02d19b45c7efcdcabdd956421b1e449e771fca0b0f072e02d7aa65ebb29f23 SIZE (smarco-WFA2-lib-v2.3.4_GH0.tar.gz) = 4224505
Packages (timestamps in pop-ups are UTC):
wfa2-lib
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.3.42.3.4-2.3.42.3.4---
FreeBSD:13:quarterly2.3.42.3.42.3.2_12.3.42.3.42.3.42.3.42.3.4
FreeBSD:14:latest2.3.42.3.4-2.3.42.3.42.3.2_1-2.3.2_1
FreeBSD:14:quarterly2.3.42.3.4-2.3.42.3.42.3.42.3.42.3.4
FreeBSD:15:latest2.3.42.3.4n/a2.3.4n/a2.3.42.3.42.3.4
FreeBSD:15:quarterly--n/a-n/a---
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/v2.3.4?dummy=/
Collapse this list.

There are no commits on branch 2022Q2 for this port
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