[med-svn] [Git][med-team/ariba][master] 2 commits: add patch to make code work with pysam >= 0.24

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / ariba


Commits:
fc083795 by Andreas Tille at 2026-09-21T17:26:29+02:00
add patch to make code work with pysam >= 0.24

pysam 0.24.x stopped returning captured output from pysam.faidx();
write_fa_subset now uses pysam.FastaFile to fetch sequences, fixing
the FTBFS of ariba/tests/faidx_test.py::test_write_fa_subset.

- - - - -
d1142e33 by Andreas Tille at 2026-09-21T17:30:38+02:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/faidx-pysam-0.24.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,12 @@
-ariba (2.14.7+ds-14) UNRELEASED; urgency=medium
+ariba (2.14.7+ds-14) unstable; urgency=medium
 
   * Team upload.
   * d/watch: version=5
   * Standards-Version: 4.7.4 (routine-update)
   * Reflow Uploaders field (cme)
+  * Add patch to fix build failure with python3-pysam >= 0.24
 
- -- Andreas Tille <tille at debian.org>  Mon, 21 Sep 2026 14:05:00 +0200
+ -- Andreas Tille <tille at debian.org>  Mon, 21 Sep 2026 17:26:40 +0200
 
 ariba (2.14.7+ds-13) unstable; urgency=medium
 


=====================================
debian/patches/faidx-pysam-0.24.patch
=====================================
@@ -0,0 +1,26 @@
+Description: Fix write_fa_subset with pysam >= 0.24
+ pysam 0.24.x rewrote the samtools stdout redirection.  As a result
+ pysam.faidx(infile, region) no longer returns the fetched sequence as
+ a string (it returns an empty string while the sequence is written to
+ the process' real stdout), which made write_fa_subset write empty
+ output files and broke ariba/tests/faidx_test.py::test_write_fa_subset.
+ Fetch sequences via pysam.FastaFile instead, which works with all
+ supported pysam versions.
+Forwarded: no
+Last-Update: 2026-09-21
+
+--- a/ariba/faidx.py
++++ b/ariba/faidx.py
+@@ -8,7 +8,10 @@
+         pysam.faidx(infile)
+ 
+     f = pyfastaq.utils.open_file_write(outfile)
+-    for name in seq_names:
+-        print(pysam.faidx(infile, name), end='', file=f)
++    with pysam.FastaFile(infile) as fasta:
++        for name in seq_names:
++            seq = fasta.fetch(name)
++            print('>' + name, file=f)
++            print(seq, file=f)
+     pyfastaq.utils.close(f)
+ 


=====================================
debian/patches/series
=====================================
@@ -9,3 +9,4 @@ python3.12_syntax_warning.patch
 py3.13.patch
 remove_pkg_resources.patch
 multiprocessing-py3.14.patch
+faidx-pysam-0.24.patch



View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/acab067d3aef47394d26cf48034a7c389792b048...d1142e3304a5677924adbd7bf189c2030554280a

-- 
View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/acab067d3aef47394d26cf48034a7c389792b048...d1142e3304a5677924adbd7bf189c2030554280a
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