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from b8fd88f Upload to unstable new 1520aab Imported Upstream version 0.11.2.2+ds new 21a9d04 Merge tag 'upstream/0.11.2.2+ds' new 3a8f314 Update patches new 6f6eeae Bump htslib/samtools/bcftools minimum version requirements The 4 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: .gitignore | 14 +- MANIFEST.in | 7 +- bcftools/HMM.c | 141 +- bcftools/HMM.c.pysam.c | 141 +- bcftools/HMM.h | 26 +- {samtools => bcftools}/bam2bcf.c | 54 +- {samtools => bcftools}/bam2bcf.c.pysam.c | 54 +- {samtools => bcftools}/bam2bcf.h | 7 +- {samtools => bcftools}/bam2bcf_indel.c | 141 +- {samtools => bcftools}/bam2bcf_indel.c.pysam.c | 141 +- bcftools/bam_sample.c | 393 ++ bcftools/bam_sample.c.pysam.c | 395 ++ samtools/errmod.h => bcftools/bam_sample.h | 41 +- bcftools/bcftools.h | 1 + bcftools/bin.c | 104 + bcftools/bin.c.pysam.c | 106 + bcftools/{gvcf.h => bin.h} | 48 +- bcftools/call.h | 3 +- bcftools/ccall.c | 10 +- bcftools/ccall.c.pysam.c | 10 +- bcftools/consensus.c | 56 +- bcftools/consensus.c.pysam.c | 56 +- bcftools/convert.c | 490 ++- bcftools/convert.c.pysam.c | 490 ++- bcftools/csq.c | 3824 +++++++++++++++++++ bcftools/csq.c.pysam.c | 3826 ++++++++++++++++++++ bcftools/filter.c | 357 +- bcftools/filter.c.pysam.c | 357 +- bcftools/hclust.c | 400 ++ bcftools/hclust.c.pysam.c | 402 ++ bcftools/hclust.h | 77 + bcftools/kheap.h | 171 + bcftools/main.c | 10 + bcftools/main.c.pysam.c | 10 + bcftools/mcall.c | 228 +- bcftools/mcall.c.pysam.c | 228 +- bcftools/mpileup.c | 1110 ++++++ bcftools/mpileup.c.pysam.c | 1112 ++++++ bcftools/mw.h | 1944 ++++++++++ bcftools/ploidy.c | 22 +- bcftools/ploidy.c.pysam.c | 22 +- bcftools/ploidy.h | 2 +- bcftools/prob1.c | 12 +- bcftools/prob1.c.pysam.c | 12 +- bcftools/prob1.h | 2 +- bcftools/regidx.c | 598 +++ bcftools/regidx.c.pysam.c | 600 +++ bcftools/regidx.h | 191 + bcftools/smpl_ilist.c | 106 + bcftools/smpl_ilist.c.pysam.c | 108 + bcftools/smpl_ilist.h | 47 + bcftools/tabix.c | 30 +- bcftools/tabix.c.pysam.c | 30 +- bcftools/tsv2vcf.c | 1 + bcftools/tsv2vcf.c.pysam.c | 1 + bcftools/vcfannotate.c | 744 ++-- bcftools/vcfannotate.c.pysam.c | 744 ++-- bcftools/vcfcall.c | 44 +- bcftools/vcfcall.c.pysam.c | 44 +- bcftools/vcfcnv.c | 46 +- bcftools/vcfcnv.c.pysam.c | 46 +- bcftools/vcfconcat.c | 164 +- bcftools/vcfconcat.c.pysam.c | 164 +- bcftools/vcfconvert.c | 120 +- bcftools/vcfconvert.c.pysam.c | 120 +- bcftools/vcffilter.c | 3 +- bcftools/vcffilter.c.pysam.c | 3 +- bcftools/vcfgtcheck.c | 298 +- bcftools/vcfgtcheck.c.pysam.c | 298 +- bcftools/vcfindex.c | 115 +- bcftools/vcfindex.c.pysam.c | 115 +- bcftools/vcfmerge.c | 1075 ++++-- bcftools/vcfmerge.c.pysam.c | 1075 ++++-- bcftools/vcfnorm.c | 82 +- bcftools/vcfnorm.c.pysam.c | 82 +- bcftools/vcfplugin.c | 56 +- bcftools/vcfplugin.c.pysam.c | 56 +- bcftools/vcfroh.c | 961 +++-- bcftools/vcfroh.c.pysam.c | 961 +++-- bcftools/vcfstats.c | 429 ++- bcftools/vcfstats.c.pysam.c | 429 ++- bcftools/vcfview.c | 50 +- bcftools/vcfview.c.pysam.c | 50 +- bcftools/version.h | 2 +- buildwheels.sh | 2 +- debian/control | 6 +- ...de_test_tyring_to_access_remote_ftpserver.patch | 29 - debian/patches/htslib-external-config.patch | 14 +- debian/patches/rpath.patch | 10 - debian/patches/series | 1 - doc/api.rst | 4 +- doc/release.rst | 75 + doc/usage.rst | 19 +- import.py | 29 +- pysam/__init__.py | 2 + pysam/cbcftools_util.h | 6 + pysam/csamtools_util.h | 6 + pysam/htslib_util.h | 20 - pysam/libcalignedsegment.pxd | 6 - pysam/libcalignedsegment.pyx | 288 +- pysam/libcalignmentfile.pyx | 344 +- pysam/libcbcf.pxd | 21 +- pysam/libcbcf.pyx | 848 ++++- pysam/libcbcftools.pxd | 3 + pysam/libcbcftools.pyx | 2 + pysam/libcbgzf.pyx | 53 +- pysam/libcfaidx.pyx | 31 +- pysam/libchtslib.pxd | 679 +++- pysam/libchtslib.pyx | 285 +- pysam/libcsamtools.pxd | 3 + pysam/libcsamtools.pyx | 2 + pysam/libctabix.pxd | 4 + pysam/libctabix.pyx | 42 +- pysam/libctabixproxies.pxd | 14 +- pysam/libctabixproxies.pyx | 506 ++- pysam/libcutils.pxd | 4 +- pysam/libcutils.pyx | 30 +- pysam/pysam_util.c | 6 +- pysam/pysam_util.h | 4 + pysam/samfile_util.c | 172 - pysam/samfile_util.h | 3 - pysam/tabix_util.c | 1 + pysam/utils.py | 13 +- pysam/version.py | 11 +- samtools/bam.h | 2 +- samtools/bam2bcf.c | 2 +- samtools/bam2bcf.c.pysam.c | 2 +- samtools/bam2bcf.h | 2 +- samtools/bam2bcf_indel.c | 26 +- samtools/bam2bcf_indel.c.pysam.c | 26 +- samtools/bam2depth.c | 30 +- samtools/bam2depth.c.pysam.c | 30 +- samtools/bam_addrprg.c | 86 +- samtools/bam_addrprg.c.pysam.c | 86 +- samtools/bam_cat.c | 60 +- samtools/bam_cat.c.pysam.c | 60 +- samtools/bam_index.c | 52 +- samtools/bam_index.c.pysam.c | 52 +- samtools/bam_mate.c | 71 +- samtools/bam_mate.c.pysam.c | 71 +- samtools/bam_md.c | 202 +- samtools/bam_md.c.pysam.c | 204 +- samtools/bam_plcmd.c | 122 +- samtools/bam_plcmd.c.pysam.c | 122 +- samtools/bam_quickcheck.c | 52 +- samtools/bam_quickcheck.c.pysam.c | 52 +- samtools/bam_reheader.c | 4 +- samtools/bam_reheader.c.pysam.c | 14 +- samtools/bam_rmdup.c | 4 +- samtools/bam_rmdup.c.pysam.c | 4 +- samtools/bam_sort.c | 178 +- samtools/bam_sort.c.pysam.c | 178 +- samtools/bam_split.c | 99 +- samtools/bam_split.c.pysam.c | 99 +- samtools/bam_stat.c | 28 +- samtools/bam_stat.c.pysam.c | 38 +- samtools/bam_tview.c | 441 --- samtools/bam_tview.c.pysam.c | 443 --- samtools/bam_tview.h | 105 - samtools/bam_tview_curses.c | 352 -- samtools/bam_tview_curses.c.pysam.c | 354 -- samtools/bam_tview_html.c | 377 -- samtools/bam_tview_html.c.pysam.c | 379 -- samtools/bamshuf.c | 22 +- samtools/bamshuf.c.pysam.c | 22 +- samtools/bamtk.c | 35 +- samtools/bamtk.c.pysam.c | 39 +- samtools/bedcov.c | 8 +- samtools/bedcov.c.pysam.c | 8 +- samtools/cut_target.c | 19 +- samtools/cut_target.c.pysam.c | 19 +- samtools/errmod.c | 194 - samtools/errmod.c.pysam.c | 196 - samtools/faidx.c | 74 +- samtools/faidx.c.pysam.c | 74 +- samtools/kprobaln.c | 282 -- samtools/kprobaln.c.pysam.c | 284 -- samtools/kprobaln.h | 49 - samtools/misc/ace2sam.c | 5 +- samtools/misc/ace2sam.c.pysam.c | 5 +- samtools/padding.c | 4 +- samtools/padding.c.pysam.c | 4 +- samtools/phase.c | 6 +- samtools/phase.c.pysam.c | 6 +- samtools/sam.h | 2 +- samtools/sam_opts.c | 8 +- samtools/sam_opts.c.pysam.c | 8 +- samtools/sam_opts.h | 7 +- samtools/{samtools.h => sam_utils.c} | 57 +- samtools/{samtools.h => sam_utils.c.pysam.c} | 59 +- samtools/sam_view.c | 498 ++- samtools/sam_view.c.pysam.c | 500 ++- samtools/stats.c | 20 +- samtools/stats.c.pysam.c | 29 +- samtools/test/split/test_filter_header_rg.c | 15 +- .../test/split/test_filter_header_rg.c.pysam.c | 15 +- samtools/test/test.c | 8 +- samtools/test/test.c.pysam.c | 8 +- samtools/version.h | 2 +- setup.py | 69 +- tests/AlignedSegment_test.py | 93 +- tests/AlignmentFile_test.py | 143 +- tests/SamFile_test.py | 1990 ---------- tests/StreamFiledescriptors_test.py | 71 +- tests/TestUtils.py | 32 +- tests/VariantFile_test.py | 5 +- tests/faidx_test.py | 14 +- tests/samtools_test.py | 47 +- tests/tabix_data/example.gff2.gz | Bin 0 -> 238 bytes tests/tabix_data/example.gff2.gz.tbi | Bin 0 -> 107 bytes tests/tabix_data/example.gff3.gz | Bin 0 -> 3067 bytes tests/tabix_data/example.gff3.gz.tbi | Bin 0 -> 1457 bytes tests/tabix_test.py | 262 +- tests/tabixproxies_test.py | 318 ++ 214 files changed, 28687 insertions(+), 12200 deletions(-) copy {samtools => bcftools}/bam2bcf.c (96%) copy {samtools => bcftools}/bam2bcf.c.pysam.c (96%) copy {samtools => bcftools}/bam2bcf.h (96%) copy {samtools => bcftools}/bam2bcf_indel.c (83%) copy {samtools => bcftools}/bam2bcf_indel.c.pysam.c (83%) create mode 100644 bcftools/bam_sample.c create mode 100644 bcftools/bam_sample.c.pysam.c rename samtools/errmod.h => bcftools/bam_sample.h (53%) create mode 100644 bcftools/bin.c create mode 100644 bcftools/bin.c.pysam.c copy bcftools/{gvcf.h => bin.h} (52%) create mode 100644 bcftools/csq.c create mode 100644 bcftools/csq.c.pysam.c create mode 100644 bcftools/hclust.c create mode 100644 bcftools/hclust.c.pysam.c create mode 100644 bcftools/hclust.h create mode 100644 bcftools/kheap.h create mode 100644 bcftools/mpileup.c create mode 100644 bcftools/mpileup.c.pysam.c create mode 100644 bcftools/mw.h create mode 100644 bcftools/regidx.c create mode 100644 bcftools/regidx.c.pysam.c create mode 100644 bcftools/regidx.h create mode 100644 bcftools/smpl_ilist.c create mode 100644 bcftools/smpl_ilist.c.pysam.c create mode 100644 bcftools/smpl_ilist.h delete mode 100644 debian/patches/exclude_test_tyring_to_access_remote_ftpserver.patch create mode 100644 pysam/cbcftools_util.h create mode 100644 pysam/csamtools_util.h create mode 100644 pysam/libcbcftools.pxd create mode 100644 pysam/libcbcftools.pyx create mode 100644 pysam/libcsamtools.pxd create mode 100644 pysam/libcsamtools.pyx delete mode 100644 samtools/bam_tview.c delete mode 100644 samtools/bam_tview.c.pysam.c delete mode 100644 samtools/bam_tview.h delete mode 100644 samtools/bam_tview_curses.c delete mode 100644 samtools/bam_tview_curses.c.pysam.c delete mode 100644 samtools/bam_tview_html.c delete mode 100644 samtools/bam_tview_html.c.pysam.c delete mode 100644 samtools/errmod.c delete mode 100644 samtools/errmod.c.pysam.c delete mode 100644 samtools/kprobaln.c delete mode 100644 samtools/kprobaln.c.pysam.c delete mode 100644 samtools/kprobaln.h copy samtools/{samtools.h => sam_utils.c} (54%) copy samtools/{samtools.h => sam_utils.c.pysam.c} (53%) delete mode 100644 tests/SamFile_test.py create mode 100644 tests/tabix_data/example.gff2.gz create mode 100644 tests/tabix_data/example.gff2.gz.tbi create mode 100644 tests/tabix_data/example.gff3.gz create mode 100644 tests/tabix_data/example.gff3.gz.tbi create mode 100644 tests/tabixproxies_test.py -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pysam.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit