GNU bug report logs - #61148
[PATCH 0/5] Update vcflib

Previous Next

Full log

View this message in rfc822 format

From: Efraim Flashner <efraim <at> flashner.co.il>
To: 61148 <at> debbugs.gnu.org
Cc: Efraim Flashner <efraim <at> flashner.co.il>
Subject: [bug#61148] [PATCH 3/5] gnu: Add wfa2-lib.
Date: Sun, 29 Jan 2023 15:12:36 +0200

* gnu/packages/bioinformatics.scm (wfa2-lib): New variable.
---
 gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa0a6c0dd6..7b5d5c5e8c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15710,6 +15710,40 @@ (define-public tabixpp
 some of the details of opening and jumping in tabix-indexed files.")
    (license license:expat)))
 
+(define-public wfa2-lib
+  (let ((commit "188b522ae634add3c692ca7547595b7266f1fa19")
+        (revision "1"))
+    (package
+      (name "wfa2-lib")
+      (version (git-version "2.3.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/smarco/WFA2-lib")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "1pq844zsl7v5zk6pzkbh5j2k2g1ac54nlvgyihla2wlwi0ibndax"))))
+      (build-system cmake-build-system)
+      (arguments
+       (list
+         #:configure-flags
+         #~(list "-DOPENMP=ON")))
+      (native-inputs
+       (list pkg-config))
+      (home-page "https://github.com/ekg/tabixpp")
+      (synopsis "Wavefront alignment algorithm library")
+      (description "The @acronym{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 to traditional dynamic
+programming algorithms that run in quadratic time, the WFA runs in time
+@code{O(ns+s^2)}, proportional to the sequence length @code{n} and the alignment
+score @code{s}, using @code{O(s^2)} memory (or @code{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.")
+      (license license:expat))))
+
 (define-public smithwaterman
   (let ((commit "2610e259611ae4cde8f03c72499d28f03f6d38a7"))
     (package
-- 
Efraim Flashner   <efraim <at> flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.