This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository python-pysam.
commit f2ee92854ff349785e54b6e3fc0a0cf2cb62ef42 Merge: 09caf28 f470810 Author: Afif Elghraoui <[email protected]> Date: Sun Jun 19 14:18:01 2016 -0700 Merge tag 'upstream/0.9.1+ds' Upstream version 0.9.1+ds INSTALL | 2 +- bcftools/bcftools.h | 3 +- bcftools/consensus.c | 2 +- bcftools/consensus.c.pysam.c | 48 +-- bcftools/convert.c.pysam.c | 8 +- bcftools/em.c.pysam.c | 8 +- bcftools/filter.c.pysam.c | 22 +- bcftools/khash_str2str.h | 19 +- bcftools/main.c | 4 +- bcftools/main.c.pysam.c | 18 +- bcftools/mcall.c.pysam.c | 20 +- bcftools/ploidy.c | 30 +- bcftools/ploidy.c.pysam.c | 30 +- bcftools/prob1.c.pysam.c | 8 +- bcftools/pysam.h | 4 +- bcftools/tabix.c.pysam.c | 34 +- bcftools/vcfannotate.c | 212 ++++++++++-- bcftools/vcfannotate.c.pysam.c | 256 +++++++++++---- bcftools/vcfcall.c | 43 ++- bcftools/vcfcall.c.pysam.c | 155 +++++---- bcftools/vcfcnv.c.pysam.c | 84 ++--- bcftools/vcfconcat.c | 139 +++++++- bcftools/vcfconcat.c.pysam.c | 187 +++++++++-- bcftools/vcfconvert.c | 18 +- bcftools/vcfconvert.c.pysam.c | 196 +++++------ bcftools/vcffilter.c | 8 +- bcftools/vcffilter.c.pysam.c | 50 +-- bcftools/vcfgtcheck.c.pysam.c | 52 +-- bcftools/vcfindex.c | 3 +- bcftools/vcfindex.c.pysam.c | 67 ++-- bcftools/vcfisec.c | 12 +- bcftools/vcfisec.c.pysam.c | 84 ++--- bcftools/vcfmerge.c | 10 +- bcftools/vcfmerge.c.pysam.c | 96 +++--- bcftools/vcfnorm.c | 20 +- bcftools/vcfnorm.c.pysam.c | 76 +++-- bcftools/vcfplugin.c | 41 +-- bcftools/vcfplugin.c.pysam.c | 127 ++++---- bcftools/vcfquery.c.pysam.c | 52 +-- bcftools/vcfroh.c | 43 ++- bcftools/vcfroh.c.pysam.c | 107 +++--- bcftools/vcfsom.c.pysam.c | 56 ++-- bcftools/vcfstats.c.pysam.c | 242 +++++++------- bcftools/vcfview.c | 8 +- bcftools/vcfview.c.pysam.c | 102 +++--- bcftools/version.c.pysam.c | 2 +- bcftools/version.h | 2 +- doc/faq.rst | 2 +- doc/glossary.rst | 3 +- doc/installation.rst | 5 - doc/release.rst | 20 ++ import.py | 82 ++++- pysam/__init__.py | 2 + pysam/calignedsegment.pyx | 127 +++++++- pysam/calignmentfile.pxd | 1 + pysam/calignmentfile.pyx | 41 ++- pysam/cbcf.pyx | 2 +- pysam/cfaidx.pxd | 12 +- pysam/cfaidx.pyx | 44 ++- pysam/chtslib.pxd | 39 ++- pysam/ctabix.pxd | 13 +- pysam/ctabix.pyx | 27 +- pysam/ctabixproxies.pyx | 68 +++- pysam/cutils.pxd | 3 + pysam/cutils.pyx | 212 +++++------- pysam/cvcf.pyx | 13 +- pysam/pysam_stream.h | 3 +- pysam/pysam_util.c | 50 ++- pysam/pysam_util.h | 19 +- pysam/tabix_util.c | 2 - pysam/utils.py | 20 +- pysam/version.py | 6 +- run_tests_travis.sh | 30 +- samtools/bam.c | 18 +- samtools/bam.c.pysam.c | 18 +- samtools/bam.h | 9 +- samtools/bam2bcf.c | 2 + samtools/bam2bcf.c.pysam.c | 10 +- samtools/bam2bcf_indel.c | 2 + samtools/bam2bcf_indel.c.pysam.c | 22 +- samtools/bam2depth.c | 2 + samtools/bam2depth.c.pysam.c | 70 ++-- samtools/bam_addrprg.c | 2 + samtools/bam_addrprg.c.pysam.c | 42 +-- samtools/bam_aux.c | 2 + samtools/bam_aux.c.pysam.c | 2 + samtools/bam_cat.c | 93 ++++-- samtools/bam_cat.c.pysam.c | 121 ++++--- samtools/bam_color.c | 2 + samtools/bam_color.c.pysam.c | 2 + samtools/bam_flags.c | 2 + samtools/bam_flags.c.pysam.c | 42 +-- samtools/bam_import.c | 2 + samtools/bam_import.c.pysam.c | 4 +- samtools/bam_index.c | 2 + samtools/bam_index.c.pysam.c | 20 +- samtools/bam_lpileup.c | 2 + samtools/bam_lpileup.c.pysam.c | 12 +- samtools/bam_mate.c | 80 +++-- samtools/bam_mate.c.pysam.c | 88 +++-- samtools/bam_md.c | 64 +++- samtools/bam_md.c.pysam.c | 84 +++-- samtools/bam_plbuf.c | 2 + samtools/bam_plbuf.c.pysam.c | 2 + samtools/bam_plcmd.c | 6 +- samtools/bam_plcmd.c.pysam.c | 74 +++-- samtools/bam_quickcheck.c | 22 +- samtools/bam_quickcheck.c.pysam.c | 48 ++- samtools/bam_reheader.c | 64 +++- samtools/bam_reheader.c.pysam.c | 95 ++++-- samtools/bam_rmdup.c | 109 +++++-- samtools/bam_rmdup.c.pysam.c | 129 ++++++-- samtools/bam_rmdupse.c | 64 +++- samtools/bam_rmdupse.c.pysam.c | 66 +++- samtools/bam_sort.c | 267 ++++++++++----- samtools/bam_sort.c.pysam.c | 329 +++++++++++++------ samtools/bam_split.c | 88 +++-- samtools/bam_split.c.pysam.c | 124 ++++--- samtools/bam_stat.c | 2 + samtools/bam_stat.c.pysam.c | 46 +-- samtools/bam_tview.c | 2 + samtools/bam_tview.c.pysam.c | 18 +- samtools/bam_tview_curses.c.pysam.c | 2 +- samtools/bam_tview_html.c | 2 + samtools/bam_tview_html.c.pysam.c | 8 +- samtools/bamshuf.c | 141 ++++++-- samtools/bamshuf.c.pysam.c | 163 +++++++--- samtools/bamtk.c | 6 +- samtools/bamtk.c.pysam.c | 36 +- samtools/bedcov.c | 2 + samtools/bedcov.c.pysam.c | 16 +- samtools/bedidx.c | 2 + samtools/bedidx.c.pysam.c | 6 +- samtools/cut_target.c | 2 + samtools/cut_target.c.pysam.c | 24 +- samtools/dict.c | 5 +- samtools/dict.c.pysam.c | 29 +- samtools/errmod.c | 2 + samtools/errmod.c.pysam.c | 2 + samtools/faidx.c | 6 +- samtools/faidx.c.pysam.c | 20 +- samtools/kprobaln.c | 2 + samtools/kprobaln.c.pysam.c | 14 +- samtools/misc/ace2sam.c | 2 + samtools/misc/ace2sam.c.pysam.c | 38 ++- samtools/padding.c | 42 ++- samtools/padding.c.pysam.c | 136 ++++---- samtools/phase.c | 89 +++-- samtools/phase.c.pysam.c | 167 ++++++---- samtools/pysam.h | 4 +- samtools/sam.c | 18 +- samtools/sam.c.pysam.c | 26 +- samtools/sam_header.c | 2 + samtools/sam_header.c.pysam.c | 8 +- samtools/sam_opts.c | 2 + samtools/sam_opts.c.pysam.c | 4 +- samtools/sam_view.c | 84 +++-- samtools/sam_view.c.pysam.c | 152 +++++---- samtools/sample.c | 2 + samtools/sample.c.pysam.c | 2 + samtools/stats.c | 2 + samtools/stats.c.pysam.c | 60 ++-- samtools/stats_isize.c | 2 + samtools/stats_isize.c.pysam.c | 4 +- samtools/test/merge/test_bam_translate.c | 2 + samtools/test/merge/test_bam_translate.c.pysam.c | 170 +++++----- samtools/test/merge/test_rtrans_build.c | 2 + samtools/test/merge/test_rtrans_build.c.pysam.c | 26 +- samtools/test/merge/test_trans_tbl_init.c | 16 +- samtools/test/merge/test_trans_tbl_init.c.pysam.c | 152 ++++----- samtools/test/split/test_count_rg.c | 2 + samtools/test/split/test_count_rg.c.pysam.c | 32 +- samtools/test/split/test_expand_format_string.c | 2 + .../test/split/test_expand_format_string.c.pysam.c | 32 +- samtools/test/split/test_filter_header_rg.c | 2 + .../test/split/test_filter_header_rg.c.pysam.c | 50 +-- samtools/test/split/test_parse_args.c | 2 + samtools/test/split/test_parse_args.c.pysam.c | 120 +++---- samtools/test/test.c | 2 + samtools/test/test.c.pysam.c | 16 +- samtools/test/tview/test_get_rg_sample.c | 2 + samtools/test/tview/test_get_rg_sample.c.pysam.c | 6 +- samtools/version.h | 2 +- setup.py | 27 +- tests/AlignedSegment_test.py | 121 ++++++- tests/AlignmentFile_test.py | 362 +++++++++++---------- tests/TestUtils.py | 34 +- tests/VariantFile_test.py | 47 ++- tests/cbcf_data/example_vcf42.vcf | 6 +- tests/faidx_test.py | 63 +++- tests/pysam_data/Makefile | 9 +- tests/samtools_test.py | 82 ++++- tests/tabix_test.py | 145 ++++++--- tests/test_samtools_python.py | 35 ++ 194 files changed, 5846 insertions(+), 3093 deletions(-) -- Alioth's 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