[med-svn] [python-pbcore] 03/06: Merge tag 'upstream/1.2.6+dfsg'

[Afif Elghraoui]

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

commit 9f4ca8988dc7f203259cab1737950ee1add4c26e
Merge: 49aebd5 56e8b41
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Nov 26 13:47:18 2015 -0800

    Merge tag 'upstream/1.2.6+dfsg'
    
    Upstream version 1.2.6+dfsg

 .circleci/installHDF5.sh               |   14 -
 .gitignore                             |   13 -
 CHANGELOG.org                          |    7 +
 PKG-INFO                               |   69 ++
 pbcore.egg-info/PKG-INFO               |   69 ++
 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 +
 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 +-
 39 files changed, 4215 insertions(+), 2985 deletions(-)

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