From: Étienne Mollier Date: Wed, 29 May 2024 11:21:22 +0000 (+0200) Subject: htslib-1.20.patch: new: anticipate test failure. X-Git-Tag: archive/raspbian/0.23.0+ds-1+rpi1~1^2~6 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=95a63e2a23d390508e0057f00b1f36df07888008;p=python-pysam.git 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 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 +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 43ee385..468debd 100644 --- 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