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commit 1bd6baee22547147bf3c5ff6b48251aa2e0f8606 Merge: ed944ba 91c30fd Author: Afif Elghraoui <a...@ghraoui.name> Date: Sun Jun 7 22:30:07 2015 -0700 Merge tag 'upstream/0.8.3' Upstream version 0.8.3 .gitignore | 2 +- AUTHORS | 10 +- INSTALL | 2 +- MANIFEST.in | 2 +- doc/api.rst | 13 +- doc/conf.py | 2 +- doc/developer.rst | 17 +- doc/faq.rst | 85 +- doc/index.rst | 2 +- doc/release.rst | 61 +- doc/usage.rst | 14 +- htslib/INSTALL | 88 +- htslib/Makefile | 93 +- htslib/NEWS | 50 + htslib/bgzf.c | 58 +- htslib/bgzip.c | 2 +- htslib/config.mk | 72 + htslib/config.mk.in | 72 + htslib/configure | 4012 +++++++++++++++++++++ htslib/configure.ac | 93 + htslib/cram/cram.h | 9 +- htslib/cram/cram_codecs.c | 230 +- htslib/cram/cram_codecs.h | 22 +- htslib/cram/cram_decode.c | 1339 +++++-- htslib/cram/cram_encode.c | 1994 ++++++---- htslib/cram/cram_index.c | 82 +- htslib/cram/cram_io.c | 1382 ++++--- htslib/cram/cram_io.h | 98 +- htslib/cram/cram_samtools.c | 5 +- htslib/cram/cram_stats.c | 123 +- htslib/cram/cram_structs.h | 329 +- htslib/cram/os.h | 2 + htslib/cram/rANS_byte.h | 336 ++ htslib/cram/rANS_static.c | 841 +++++ htslib/cram/rANS_static.h | 44 + htslib/cram/sam_header.c | 8 +- htslib/cram/sam_header.h | 8 - htslib/cram/thread_pool.c | 178 +- htslib/cram/thread_pool.h | 15 +- htslib/cram/vlen.c | 2 +- htslib/faidx.c | 46 +- htslib/hfile.c | 23 +- htslib/hfile_internal.h | 3 +- htslib/hfile_irods.c | 243 ++ htslib/hts.c | 531 ++- htslib/htsfile.1 | 71 + htslib/htsfile.c | 168 + htslib/htslib.mk | 8 +- htslib/htslib/bgzf.h | 7 +- htslib/htslib/faidx.h | 2 +- htslib/htslib/hfile.h | 10 +- htslib/htslib/hts.h | 146 +- htslib/htslib/khash.h | 8 +- htslib/htslib/khash_str2int.h | 9 + htslib/htslib/kseq.h | 10 +- htslib/htslib/regidx.h | 147 + htslib/htslib/sam.h | 2 +- htslib/htslib/synced_bcf_reader.h | 15 +- htslib/htslib/vcf.h | 15 +- htslib/htslib_vars.mk | 1 + htslib/knetfile.c | 11 +- htslib/regidx.c | 338 ++ htslib/sam.c | 134 +- htslib/synced_bcf_reader.c | 88 +- htslib/tabix.1 | 121 +- htslib/tabix.c | 268 +- htslib/tbx.c | 5 + htslib/test/{aux#aux.sam => auxf#values.sam} | 0 htslib/test/{aux.fa => auxf.fa} | 0 htslib/test/{aux.fa.fai => auxf.fa.fai} | 0 htslib/test/hfile.c | 4 +- htslib/test/sam.c | 52 +- htslib/test/test-regidx.c | 116 + htslib/test/test-vcf-api.c | 57 +- htslib/test/test_view.c | 92 +- htslib/vcf.c | 207 +- htslib/vcfutils.c | 63 +- htslib/version.h | 2 +- install-CGAT-tools.sh | 8 +- pysam/TabProxies.pyx | 142 +- pysam/__init__.py | 10 +- pysam/calignmentfile.pxd | 30 +- pysam/calignmentfile.pyx | 1109 ++++-- pysam/cbcf.pxd | 158 + pysam/cbcf.pyx | 2419 +++++++++++++ pysam/cfaidx.pxd | 9 +- pysam/cfaidx.pyx | 39 +- pysam/chtslib.pxd | 891 ++++- pysam/chtslib.pyx | 2 +- pysam/csamtools.pyx | 2 + pysam/ctabix.pyx | 4 +- pysam/cvcf.pyx | 2 +- pysam/htslib_util.c | 18 + pysam/htslib_util.h | 20 +- pysam/version.py | 6 +- requires.txt | 2 +- samtools/bam.h | 2 +- samtools/bam2bcf_indel.c | 40 +- samtools/bam2bcf_indel.c.pysam.c | 40 +- samtools/bam2depth.c | 16 +- samtools/bam2depth.c.pysam.c | 16 +- samtools/bam_mate.c | 3 +- samtools/bam_mate.c.pysam.c | 3 +- samtools/bam_md.c | 1 - samtools/bam_md.c.pysam.c | 1 - samtools/bam_plcmd.c | 45 +- samtools/bam_plcmd.c.pysam.c | 45 +- samtools/bam_sort.c | 61 +- samtools/bam_sort.c.pysam.c | 61 +- samtools/bam_stat.c | 40 +- samtools/bam_stat.c.pysam.c | 40 +- samtools/errmod.c | 7 +- samtools/errmod.c.pysam.c | 7 +- samtools/kaln.c | 486 --- samtools/kaln.c.pysam.c | 488 --- samtools/kaln.h | 67 - samtools/misc/ace2sam.c | 2 +- samtools/misc/ace2sam.c.pysam.c | 2 +- samtools/padding.c | 2 +- samtools/padding.c.pysam.c | 2 +- samtools/sam.c | 8 +- samtools/sam.c.pysam.c | 8 +- samtools/sam.h | 3 +- samtools/sam_view.c | 27 +- samtools/sam_view.c.pysam.c | 27 +- samtools/stats.c | 21 +- samtools/stats.c.pysam.c | 21 +- samtools/test/merge/test_rtrans_build.c | 4 +- samtools/test/merge/test_rtrans_build.c.pysam.c | 4 +- samtools/test/merge/test_trans_tbl_init.c | 2 +- samtools/test/merge/test_trans_tbl_init.c.pysam.c | 2 +- samtools/version.h | 2 +- setup.py | 169 +- tests/AlignedSegment_test.py | 447 +++ tests/AlignmentFile_test.py | 1387 +++---- tests/SamFile_test.py | 14 +- tests/TestUtils.py | 72 +- tests/cython_flagstat.py | 1 - tests/pysam_data/Makefile | 13 +- tests/python_flagstat.py | 2 - tests/samtools_test.py | 45 +- tests/tabix_test.py | 7 +- 142 files changed, 18515 insertions(+), 4939 deletions(-) -- 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