htslib-1.20.patch: new: anticipate test failure.

Upcoming upload of htslib 1.20 comes with improvements causing a test
failure in pysam.  This change anticipates the correction without
introduction of regressions with existing releases of htslib.

Thanks: John Marshall

diff --git a/debian/patches/htslib-1.20.patch b/debian/patches/htslib-1.20.patch
new file mode 100644 (file)
index 0000000..63a2389
--- /dev/null
+++ b/debian/patches/htslib-1.20.patch
@@ -0,0 +1,19 @@
+Description: fix test failure with htslib 1.20.
+ This data file contains invalid data, which is diagnosed by
+ improvements in bam_parse_basemod2() in HTSlib 1.20. Updating these
+ base modification data files to the versions in htslib and hts-specs
+ corrects the problem.
+
+Author: John Marshall
+Origin: upstream, https://github.com/pysam-developers/pysam/issues/1291#issuecomment-2131146211
+Bug: https://github.com/pysam-developers/pysam/issues/1291
+Reviewed-by: Étienne Mollier <emollier@debian.org>
+Last-Update: 2024-05-29
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pysam.orig/tests/pysam_data/MM-chebi.sam
++++ python-pysam/tests/pysam_data/MM-chebi.sam
+@@ -1,2 +1,2 @@
+ @CO   Separate m, h and N modifications
+-*     0       *       0       0       *       *       0       0       AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA    *       Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15;  Ml:B:C,102,128,153,179,204,161,187,212,169
++*     0       *       0       0       *       *       0       0       AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA    *       Mm:Z:C+m,2,2,1,4,1;C+76792,6,7;N+n,15;  Ml:B:C,102,128,153,179,204,161,187,212

diff --git a/debian/patches/series b/debian/patches/series
index 43ee38595c16e3f1c81ef0d1514da8ca9eb787f0..468debd6006d8bac40a2e4fed517504970b61647 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 skip_test_remote.patch
 clean_less
 skip-test-on-32-bit.patch
+htslib-1.20.patch