[med-svn] [python-pbcore] branch master updated (a05fb4d -> 9ad012c)

[Afif Elghraoui]

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

      from  a05fb4d   python-pbcore (1.2.4+dfsg-1) unstable; urgency=medium
       new  49aebd5   Set watch file to point to pypi rather than github
       new  56e8b41   Imported Upstream version 1.2.6+dfsg
       new  9f4ca89   Merge tag 'upstream/1.2.6+dfsg'
       new  a600589   Set new changelog entry
       new  695f21f   Refresh patches
       new  9ad012c   Fix compatibility with pysam 0.8.4

The 6 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
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Summary of changes:
 .circleci/installHDF5.sh                         |   14 -
 .gitignore                                       |   13 -
 CHANGELOG.org                                    |    7 +
 LICENSES.txt => PKG-INFO                         |   12 +-
 debian/changelog                                 |    7 +
 debian/patches/enable-build-time-testing.patch   |    5 +-
 debian/patches/fix-pysam-compatibility.patch     |   36 +
 debian/patches/series                            |    1 +
 debian/watch                                     |    5 +-
 LICENSES.txt => pbcore.egg-info/PKG-INFO         |   12 +-
 pbcore.egg-info/SOURCES.txt                      |  199 +++
 pbcore.egg-info/dependency_links.txt             |    1 +
 pbcore.egg-info/entry_points.txt                 |    3 +
 pbcore.egg-info/not-zip-safe                     |    1 +
 pbcore.egg-info/pbr.json                         |    1 +
 requirements.txt => pbcore.egg-info/requires.txt |    3 +-
 pbcore.egg-info/top_level.txt                    |    1 +
 pbcore/__init__.py                               |    2 +-
 pbcore/chemistry/resources/mapping.xml           |   30 +
 pbcore/io/BasH5IO.py                             |    5 +-
 pbcore/io/align/BamAlignment.py                  |    4 +
 pbcore/io/align/BamIO.py                         |   12 +
 pbcore/io/align/CmpH5IO.py                       |    4 +
 pbcore/io/align/PacBioBamIndex.py                |    6 +-
 pbcore/io/align/_AlignmentMixin.py               |   13 +
 pbcore/io/dataset/DataSetIO.py                   |  189 +-
 pbcore/io/dataset/DataSetMembers.py              |   54 +-
 pbcore/io/dataset/DataSetReader.py               |   14 +-
 pbcore/io/dataset/DataSetValidator.py            |    2 +
 pbcore/io/dataset/DataSetWriter.py               |   85 +-
 pbcore/io/dataset/DataSetXsd.py                  |  501 +++---
 pbcore/io/dataset/EntryPoints.py                 |    3 +
 pbcore/io/dataset/__init__.py                    |   16 -
 pbcore/io/dataset/_pbbase.py                     | 2042 ++++++++++++----------
 pbcore/io/dataset/_pbds.py                       | 1898 +++++++++++---------
 pbcore/io/dataset/_pbmeta.py                     |  620 ++++---
 pbcore/io/dataset/_pbpn.py                       |  628 +++++--
 pbcore/io/dataset/_pbrk.py                       |  410 ++---
 pbcore/io/dataset/_pbsample.py                   |  132 +-
 pbcore/io/dataset/utils.py                       |    3 +
 setup.cfg                                        |    6 +
 tests/test_pbcore_io_AlnFileReaders.py           |    7 +
 tests/test_pbdataset.py                          |   62 +-
 tests/test_pbdataset_subtypes.py                 |   71 +-
 44 files changed, 4146 insertions(+), 2994 deletions(-)
 delete mode 100644 .circleci/installHDF5.sh
 delete mode 100644 .gitignore
 copy LICENSES.txt => PKG-INFO (90%)
 create mode 100644 debian/patches/fix-pysam-compatibility.patch
 copy LICENSES.txt => pbcore.egg-info/PKG-INFO (90%)
 create mode 100644 pbcore.egg-info/SOURCES.txt
 create mode 100644 pbcore.egg-info/dependency_links.txt
 create mode 100644 pbcore.egg-info/entry_points.txt
 create mode 100644 pbcore.egg-info/not-zip-safe
 create mode 100644 pbcore.egg-info/pbr.json
 copy requirements.txt => pbcore.egg-info/requires.txt (86%)
 create mode 100644 pbcore.egg-info/top_level.txt

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