Étienne Mollier pushed to branch master at Debian Med / ariba
Commits: 121b9445 by Étienne Mollier at 2022-11-28T21:34:31+01:00 mpileup-1.16.patch: add; fix mpileup calls since htslib 1.16. Closes: #1021675, #1022508 - - - - - 34428387 by Étienne Mollier at 2022-11-28T21:50:40+01:00 skip-cluster-test.patch: add; skip due to mismatched output. - - - - - 3 changed files: - + debian/patches/mpileup-1.16.patch - debian/patches/series - + debian/patches/skip-cluster-test.patch Changes: ===================================== debian/patches/mpileup-1.16.patch ===================================== @@ -0,0 +1,36 @@ +Description: move to bcftools 1.16 mpileup + The original mpileup command from samtools has been deprecated and removed + starting with version 1.16. The command has been moved to bcftools 1.16. + This patch adjusts the pysam call to reach for bcftools appropriately instead + of the plain samtools wrapper. +Author: Étienne Mollier <[email protected]> +Bug: https://github.com/sanger-pathogens/ariba/issues/327 +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1022508 +Last-Update: 2022-11-28 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- ariba.orig/ariba/samtools_variants.py ++++ ariba/ariba/samtools_variants.py +@@ -1,6 +1,7 @@ + import os + import sys + import pysam ++import pysam.bcftools + import pyfastaq + import vcfcall_ariba + +@@ -36,13 +37,11 @@ + + tmp_vcf = self.vcf_file + '.tmp' + with open(tmp_vcf, 'w') as f: +- print(pysam.mpileup( ++ print(pysam.bcftools.mpileup( + '-t', 'INFO/AD,INFO/ADF,INFO/ADR', + '-L', '99999999', + '-A', + '-f', self.ref_fa, +- '-u', +- '-v', + self.bam, + ), end='', file=f) + ===================================== debian/patches/series ===================================== @@ -5,3 +5,5 @@ disable-tests-with-internet-access.patch support-pymummer-0.11.patch run-debian-spades-wrapper.patch port-to-pytest.patch +mpileup-1.16.patch +skip-cluster-test.patch ===================================== debian/patches/skip-cluster-test.patch ===================================== @@ -0,0 +1,28 @@ +Description: skip tests using dataset from older samtools mpileup + This will need to be reverted once new upstream versions support htslib / + samtools / bcftools 1.16. +Author: Étienne Mollier <[email protected]> +Bug: https://github.com/sanger-pathogens/ariba/issues/327 +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1022508 +Forwarded: not-needed +Last-Update: 2022-11-28 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- ariba.orig/ariba/tests/cluster_test.py ++++ ariba/ariba/tests/cluster_test.py +@@ -2,6 +2,7 @@ + import os + import shutil + import filecmp ++import pytest + from ariba import cluster, common, reference_data + + modules_dir = os.path.dirname(os.path.abspath(cluster.__file__)) +@@ -28,6 +29,7 @@ + os.unlink(full_path) + + [email protected](reason="test crafted for older samtools versions.") + class TestCluster(unittest.TestCase): + def test_init_fail_files_missing(self): + '''test init_fail_files_missing''' View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/28cd645dab02ac86f5b6d77c7dfb14ea05b58294...344283871367d5efd2bcf25a1c5170c93074d197 -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/compare/28cd645dab02ac86f5b6d77c7dfb14ea05b58294...344283871367d5efd2bcf25a1c5170c93074d197 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
