Andreas Tille pushed to branch upstream at Debian Med / python-pysam
Commits: fa562021 by Andreas Tille at 2026-09-16T16:17:42+02:00 New upstream version 0.24.1+ds - - - - - 267 changed files: - NEWS - README.rst - bcftools/HMM.c - bcftools/HMM.c.pysam.c - bcftools/HMM.h - bcftools/abuf.c - bcftools/abuf.c.pysam.c - bcftools/bam2bcf.c - bcftools/bam2bcf.c.pysam.c - bcftools/bam2bcf.h - bcftools/bam2bcf_iaux.c - bcftools/bam2bcf_iaux.c.pysam.c - bcftools/bam2bcf_indel.c - bcftools/bam2bcf_indel.c.pysam.c - bcftools/bam_sample.c - bcftools/bam_sample.c.pysam.c - bcftools/bcftools.h - bcftools/bcftools.pysam.h - bcftools/bin.c - bcftools/bin.c.pysam.c - bcftools/ccall.c - bcftools/ccall.c.pysam.c - bcftools/consensus.c - bcftools/consensus.c.pysam.c - bcftools/convert.c - bcftools/convert.c.pysam.c - bcftools/csq.c - bcftools/csq.c.pysam.c - bcftools/dist.c - bcftools/dist.c.pysam.c - bcftools/filter.c - bcftools/filter.c.pysam.c - bcftools/gff.c - bcftools/gff.c.pysam.c - bcftools/gff.h - bcftools/hex.h - bcftools/main.c - bcftools/main.c.pysam.c - bcftools/mcall.c - bcftools/mcall.c.pysam.c - bcftools/mpileup.c - bcftools/mpileup.c.pysam.c - bcftools/ploidy.c - bcftools/ploidy.c.pysam.c - bcftools/ploidy.h - bcftools/rbuf.h - bcftools/read_consensus.c - bcftools/read_consensus.c.pysam.c - bcftools/regidx.c - bcftools/regidx.c.pysam.c - bcftools/regidx.h - bcftools/reheader.c - bcftools/reheader.c.pysam.c - bcftools/smpl_ilist.c - bcftools/smpl_ilist.c.pysam.c - bcftools/str_finder.c - bcftools/str_finder.c.pysam.c - bcftools/tabix.c - bcftools/tabix.c.pysam.c - bcftools/tsv2vcf.c - bcftools/tsv2vcf.c.pysam.c - bcftools/tsv2vcf.h - bcftools/variantkey.h - bcftools/vcfannotate.c - bcftools/vcfannotate.c.pysam.c - bcftools/vcfbuf.c - bcftools/vcfbuf.c.pysam.c - bcftools/vcfbuf.h - bcftools/vcfcall.c - bcftools/vcfcall.c.pysam.c - bcftools/vcfcnv.c - bcftools/vcfcnv.c.pysam.c - bcftools/vcfconcat.c - bcftools/vcfconcat.c.pysam.c - bcftools/vcfconvert.c - bcftools/vcfconvert.c.pysam.c - bcftools/vcffilter.c - bcftools/vcffilter.c.pysam.c - bcftools/vcfgtcheck.c - bcftools/vcfgtcheck.c.pysam.c - bcftools/vcfhead.c - bcftools/vcfhead.c.pysam.c - bcftools/vcfindex.c - bcftools/vcfindex.c.pysam.c - bcftools/vcfisec.c - bcftools/vcfisec.c.pysam.c - bcftools/vcfmerge.c - bcftools/vcfmerge.c.pysam.c - bcftools/vcfnorm.c - bcftools/vcfnorm.c.pysam.c - bcftools/vcfplugin.c - bcftools/vcfplugin.c.pysam.c - bcftools/vcfquery.c - bcftools/vcfquery.c.pysam.c - bcftools/vcfroh.c - bcftools/vcfroh.c.pysam.c - bcftools/vcfsort.c - bcftools/vcfsort.c.pysam.c - bcftools/vcfstats.c - bcftools/vcfstats.c.pysam.c - bcftools/vcfview.c - bcftools/vcfview.c.pysam.c - bcftools/vcmp.c - bcftools/vcmp.c.pysam.c - bcftools/version.c - bcftools/version.c.pysam.c - bcftools/version.sh - devtools/check-platform.sh - devtools/import.py - devtools/install-prerequisites.sh - doc/api.rst - doc/conf.py - doc/developer.rst - doc/faq.rst - doc/glossary.rst - doc/index.rst - doc/installation.rst - doc/requirements-rtd.txt - doc/usage.rst - import/pysam.h - linker_tests/link_pre_489/cy_build.py - linker_tests/link_pre_489/tests/test_module.py - linker_tests/link_with_rpath/tests/test_module.py - linker_tests/link_without_rpath/tests/test_module.py - pyproject.toml - pysam/Pileup.py - − pysam/cbcftools_util.h - − pysam/csamtools_util.h - + pysam/dynamic_curl.h - + pysam/dynamic_libs.c - + pysam/dynamic_openssl.h - pysam/htslib_util.c - pysam/htslib_util.h - pysam/libcalignedsegment.pxd - pysam/libcalignedsegment.pyi - pysam/libcalignedsegment.pyx - pysam/libcalignmentfile.pxd - pysam/libcalignmentfile.pyi - pysam/libcalignmentfile.pyx - pysam/libcbcf.pyi - pysam/libcbcf.pyx - pysam/libcbgzf.pyi - pysam/libcbgzf.pyx - pysam/libcfaidx.pxd - pysam/libcfaidx.pyi - pysam/libcfaidx.pyx - pysam/libchtslib.pxd - pysam/libchtslib.pyi - pysam/libchtslib.pyx - pysam/libcsamfile.pyx - pysam/libctabix.pxd - pysam/libctabix.pyi - pysam/libctabix.pyx - pysam/libctabixproxies.pyx - pysam/libcutils.pxd - pysam/libcutils.pyx - pysam/libcvcf.pxd - pysam/libcvcf.pyx - − pysam/pysam_stream.h - − pysam/pysam_util.c - − pysam/pysam_util.h - pysam/samtools.py - pysam/version.h - pysam/version.py - requirements-dev.txt - samtools/LICENSE - samtools/README - samtools/amplicon_stats.c - samtools/amplicon_stats.c.pysam.c - samtools/bam.c - samtools/bam.c.pysam.c - samtools/bam.h - samtools/bam2depth.c - samtools/bam2depth.c.pysam.c - samtools/bam_addrprg.c - samtools/bam_addrprg.c.pysam.c - samtools/bam_ampliconclip.c - samtools/bam_ampliconclip.c.pysam.c - + samtools/bam_checksum.c - + samtools/bam_checksum.c.pysam.c - samtools/bam_consensus.c - samtools/bam_consensus.c.pysam.c - + samtools/bam_consensus_tab.h - samtools/bam_fastq.c - samtools/bam_fastq.c.pysam.c - samtools/bam_import.c - samtools/bam_import.c.pysam.c - samtools/bam_index.c - samtools/bam_index.c.pysam.c - samtools/bam_markdup.c - samtools/bam_markdup.c.pysam.c - samtools/bam_mate.c - samtools/bam_mate.c.pysam.c - samtools/bam_md.c - samtools/bam_md.c.pysam.c - samtools/bam_plcmd.c - samtools/bam_plcmd.c.pysam.c - samtools/bam_reheader.c - samtools/bam_reheader.c.pysam.c - samtools/bam_sort.c - samtools/bam_sort.c.pysam.c - samtools/bam_split.c - samtools/bam_split.c.pysam.c - samtools/bamtk.c - samtools/bamtk.c.pysam.c - samtools/bedcov.c - samtools/bedcov.c.pysam.c - samtools/bedidx.c - samtools/bedidx.c.pysam.c - samtools/bedidx.h - samtools/consensus_pileup.c - samtools/consensus_pileup.c.pysam.c - samtools/consensus_pileup.h - samtools/coverage.c - samtools/coverage.c.pysam.c - samtools/cram_size.c - samtools/cram_size.c.pysam.c - samtools/dict.c - samtools/dict.c.pysam.c - samtools/faidx.c - samtools/faidx.c.pysam.c - samtools/padding.c - samtools/padding.c.pysam.c - samtools/phase.c - samtools/phase.c.pysam.c - samtools/reset.c - samtools/reset.c.pysam.c - samtools/sam_opts.c - samtools/sam_opts.c.pysam.c - samtools/sam_opts.h - samtools/sam_utils.h - samtools/sam_view.c - samtools/sam_view.c.pysam.c - samtools/samtools.h - samtools/samtools.pysam.h - samtools/stats.c - samtools/stats.c.pysam.c - samtools/version.sh - setup.cfg - setup.py - tests/AlignedSegment_bench.py - tests/AlignedSegment_test.py - tests/AlignmentFileFetchTestUtils.py - tests/AlignmentFileFetch_bench.py - tests/AlignmentFileHeader_test.py - tests/AlignmentFilePileup_bench.py - tests/AlignmentFilePileup_test.py - tests/AlignmentFile_test.py - tests/PileupTestUtils.py - tests/StreamFiledescriptors_test.py - tests/TestUtils.py - tests/VariantFileFetchTestUtils.py - tests/VariantFile_bench.py - tests/VariantFile_test.py - tests/VariantRecord_test.py - tests/_compile_test.pyx - tests/_compile_test.pyxbld - tests/compile_test.py - + tests/conftest.py - tests/faidx_test.py - + tests/libcutils_bench.py - tests/linking_test.py - tests/samtools_test.py - tests/tabix_bench.py - tests/tabix_test.py - tests/tabixproxies_test.py - tests/typechecking_test.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/commit/fa5620218821cfb91c57b70a5344c2ec0b34a3d1 -- View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/commit/fa5620218821cfb91c57b70a5344c2ec0b34a3d1 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
