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afif-guest pushed a change to branch master
in repository python-pysam.

      from  ed944ba   Removed unused paragraphs.
       new  91c30fd   Imported Upstream version 0.8.3
       new  1bd6bae   Merge tag 'upstream/0.8.3'
       new  1655f1b   Fix debian/watch
       new  4d54939   Remove unnecessary test-suite declaration in d/control
       new  a15c155   Remove nonexistent files from copyright explanations
       new  60a7bf9   override dh_auto_clean to remove .pybuild directory after 
first build
       new  d2c6f88   Update package version in d/changelog
       new  eabcdea   Allow building of the package when non-ASCII characters 
are in the path

The 8 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                                        |    2 +-
 AUTHORS                                           |   10 +-
 INSTALL                                           |    2 +-
 MANIFEST.in                                       |    2 +-
 debian/changelog                                  |    7 +-
 debian/control                                    |    1 -
 debian/copyright                                  |    2 +-
 debian/rules                                      |    6 +-
 debian/watch                                      |    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 +-
 147 files changed, 18527 insertions(+), 4945 deletions(-)
 create mode 100644 htslib/NEWS
 create mode 100644 htslib/config.mk
 create mode 100644 htslib/config.mk.in
 create mode 100755 htslib/configure
 create mode 100644 htslib/configure.ac
 create mode 100644 htslib/cram/rANS_byte.h
 create mode 100644 htslib/cram/rANS_static.c
 create mode 100644 htslib/cram/rANS_static.h
 create mode 100644 htslib/hfile_irods.c
 create mode 100644 htslib/htsfile.1
 create mode 100644 htslib/htsfile.c
 create mode 100644 htslib/htslib/regidx.h
 create mode 100644 htslib/regidx.c
 rename htslib/test/{aux#aux.sam => auxf#values.sam} (100%)
 rename htslib/test/{aux.fa => auxf.fa} (100%)
 rename htslib/test/{aux.fa.fai => auxf.fa.fai} (100%)
 create mode 100644 htslib/test/test-regidx.c
 create mode 100644 pysam/cbcf.pxd
 create mode 100644 pysam/cbcf.pyx
 delete mode 100644 samtools/kaln.c
 delete mode 100644 samtools/kaln.c.pysam.c
 delete mode 100644 samtools/kaln.h
 create mode 100644 tests/AlignedSegment_test.py

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