[med-svn] [Git][med-team/spades][master] 2 commits: Adapt to the libssw1 API

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / spades


Commits:
72777c57 by Andreas Tille at 2026-10-26T16:40:08+01:00
Adapt to the libssw1 API

- - - - -
46e8551f by Andreas Tille at 2026-10-26T17:23:23+01:00
Update d/copyright, added d/lrc.config

- - - - -


5 changed files:

- debian/changelog
- debian/copyright
- + debian/lrc.config
- + debian/patches/libssw1.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+spades (4.3.0+dfsg-2) UNRELEASED; urgency=medium
+
+  * Build against libssw1
+  * Update d/copyright, added d/lrc.config
+
+ -- Andreas Tille <tille at debian.org>  Mon, 26 Oct 2026 16:28:35 +0100
+
 spades (4.3.0+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/copyright
=====================================
@@ -94,6 +94,10 @@ Files: ext/include/pdqsort/*
 Copyright: 2015-2021 Orson Peters <orsonpeters at gmail.com>
 License: Zlib
 
+Files: ext/include/rdsl/devector.hpp
+Copyright: 2022 Valasiadis Fotios
+License: Expat
+
 Files: ext/include/samtools/*
 Copyright: 2008-2009 Genome Research Ltd.
 License: Expat
@@ -628,8 +632,8 @@ Files: src/projects/mts/stats.cpp
        src/projects/spades/pipeline/spades_pipeline/options_parser.py
        src/projects/spades/pipeline/spades_pipeline/common/*
        src/projects/spades/pipeline/spades_pipeline/executors/*
-       src/projects/spades/pipeline/spades_pipeline/scripts/copy_files.py
-       src/projects/spades/pipeline/spades_pipeline/scripts/preprocess_contigs.py
+       src/projects/spades/pipeline/spades_pipeline/supplemetary/copy_files.py
+       src/projects/spades/pipeline/spades_pipeline/supplemetary/preprocess_contigs.py
        src/projects/spades/pipeline/spades_pipeline/stages/stage.py
        src/projects/spades/pipeline/spades_pipeline/stages/terminating_stage.py
        src/projects/spades_tools/*


=====================================
debian/lrc.config
=====================================
@@ -0,0 +1,3 @@
+ext/src/bwa/bwa.1
+ext/src/bwa/LICENSE.txt
+ext/src/teamcity_gtest/LICENSE


=====================================
debian/patches/libssw1.patch
=====================================
@@ -0,0 +1,37 @@
+Description: Adapt to the libssw1 API
+ libssw 1.2.5 changed Aligner::Align() to return a uint16_t status
+ (0 on success) and made the mask length argument mandatory.
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-10-22
+Forwarded: not-needed
+Assisted-By: deepseek-v4.1-flash-free
+---
+--- a/src/common/modules/path_extend/overlap_analysis.hpp
++++ b/src/common/modules/path_extend/overlap_analysis.hpp
+@@ -80,7 +80,8 @@ class SWOverlapAnalyzer {
+             return OverlapInfo();
+         }
+         StripedSmithWaterman::Alignment alignment;
+-        if (aligner_.Align(s1.str().c_str(), s2.str().c_str(), int(s2.size()), filter_, &alignment)) {
++        if (aligner_.Align(s1.str().c_str(), s2.str().c_str(), int(s2.size()), filter_, &alignment,
++                           static_cast<int32_t>(s1.size() / 2)) == 0) {
+             if (alignment.sw_score > 0) {
+                 return OverlapInfo(Range(alignment.query_begin, alignment.query_end + 1),
+                             Range(alignment.ref_begin, alignment.ref_end + 1),
+--- a/src/projects/spades/wastewater_disentangle.cpp
++++ b/src/projects/spades/wastewater_disentangle.cpp
+@@ -295,10 +295,12 @@ namespace debruijn_graph {
+             }
+             auto seq = graph.EdgeNucls(e);
+             auto seq1_str = seq.str();
+-            aligner.Align(seq1_str.c_str(), filter, alignment1.get());
++            aligner.Align(seq1_str.c_str(), filter, alignment1.get(),
++                          static_cast<int32_t>(seq1_str.size() / 2));
+             auto seq2 = graph.EdgeNucls(graph.conjugate(e));
+             auto seq2_str = seq2.str();
+-            aligner.Align(seq2_str.c_str(), filter, alignment2.get());
++            aligner.Align(seq2_str.c_str(), filter, alignment2.get(),
++                          static_cast<int32_t>(seq2_str.size() / 2));
+             auto alignment = alignment1->sw_score > alignment2->sw_score ? alignment1 : alignment2;
+             auto seq_str = alignment1->sw_score > alignment2->sw_score ? seq1_str : seq2_str;
+ 


=====================================
debian/patches/series
=====================================
@@ -11,3 +11,4 @@ fix-missing-functional-include.patch
 fix_config_include_paths.patch
 use_system_zlib.patch
 use_system_convertutf.patch
+libssw1.patch



View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/b33d2525db9aad9e29731b572a0ad49430542139...46e8551f551a93e1ee7a1d829602b70b74bd001a

-- 
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/b33d2525db9aad9e29731b572a0ad49430542139...46e8551f551a93e1ee7a1d829602b70b74bd001a
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