[med-svn] [Git][med-team/libseqlib][master] 2 commits: Add patch adapt_to_libssw_1.2.5.patch to build against libssw 1.2.5 (SONAME...

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / libseqlib


Commits:
45103cb6 by Andreas Tille at 2026-10-26T18:19:49+01:00
Add patch adapt_to_libssw_1.2.5.patch to build against libssw 1.2.5 (SONAME bump libssw0 -> libssw1).

- - - - -
b7ca0ba8 by Andreas Tille at 2026-10-26T18:21:56+01:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/adapt_to_libssw_1.2.5.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-libseqlib (1.2.0+dfsg-13) UNRELEASED; urgency=medium
+libseqlib (1.2.0+dfsg-13) unstable; urgency=medium
 
   [ Étienne Mollier ]
   * d/rules: do not trip blhc on packages descriptions.
@@ -7,8 +7,10 @@ libseqlib (1.2.0+dfsg-13) UNRELEASED; urgency=medium
   * Drop redundant fields from d/watch
   * Reflow Uploaders field (cme)
   * debputy lint --auto-fix (routine-update)
+  * Add patch adapt_to_libssw_1.2.5.patch to build against libssw 1.2.5
+    (SONAME bump libssw0 -> libssw1).
 
- -- Étienne Mollier <emollier at debian.org>  Wed, 05 Aug 2026 22:21:24 +0200
+ -- Andreas Tille <tille at debian.org>  Mon, 26 Oct 2026 18:20:11 +0100
 
 libseqlib (1.2.0+dfsg-12) unstable; urgency=medium
 


=====================================
debian/patches/adapt_to_libssw_1.2.5.patch
=====================================
@@ -0,0 +1,20 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-10-26
+Description: Adapt to the libssw 1.2.5 API
+ libssw 1.2.5 made the mask length argument of Aligner::Align() mandatory
+ and changed its return value to a uint16_t status (0 on success).
+Forwarded: not-needed
+Assisted-By: aim2balance.ai/a2b-code
+
+--- a/src/BamRecord.cpp
++++ b/src/BamRecord.cpp
+@@ -148,7 +148,8 @@ namespace SeqLib {
+     // Declares an alignment that stores the result
+     StripedSmithWaterman::Alignment alignment;
+     // Aligns the seq to the ref
+-    aligner.Align(seq.c_str(), ref.c_str(), ref.size(), filter, &alignment);
++    aligner.Align(seq.c_str(), ref.c_str(), ref.size(), filter, &alignment,
++                  static_cast<int32_t>(seq.size()));
+ 
+     init();
+     b->core.tid = gr->chr;


=====================================
debian/patches/series
=====================================
@@ -9,3 +9,4 @@ use_debian_packaged_jsoncpp.patch
 use_debian_packaged_ssw.patch
 pkg-config.patch
 # use_private_htslib_headers.patch
+adapt_to_libssw_1.2.5.patch



View it on GitLab: https://salsa.debian.org/med-team/libseqlib/-/compare/5cc1df2d14fd9977863bbaf91685b7ce3db18fcd...b7ca0ba8303325cd71b6897153b72ee8706df996

-- 
View it on GitLab: https://salsa.debian.org/med-team/libseqlib/-/compare/5cc1df2d14fd9977863bbaf91685b7ce3db18fcd...b7ca0ba8303325cd71b6897153b72ee8706df996
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