[med-svn] [python-pbcore] 05/11: Merge tag 'upstream/1.2.2+dfsg1'

[Afif Elghraoui]

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

commit 74b076bf4fc88417a1b0d53d0e7cf0e4fa25d035
Merge: 10a2a68 cd3bf35
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Aug 10 22:55:58 2015 -0700

    Merge tag 'upstream/1.2.2+dfsg1'
    
    Upstream version 1.2.2+dfsg1

 CHANGELOG.org                                      |    7 +
 bin/dataset.py                                     |    2 +
 pbcore/__init__.py                                 |    2 +-
 pbcore/data/Makefile                               |    7 +
 pbcore/data/datasets/__init__.py                   |    6 +-
 pbcore/data/datasets/alignment.dataset.xml         |    8 +
 .../datasets/m150430_142051_Mon_p1_b25.sts.xml     |    1 +
 ...100710482550000001823136404221563_s1_p0.sts.xml |    1 +
 pbcore/data/datasets/pbalchemysim0.reference.xml   |   79 +-
 pbcore/data/datasets/subreadSetWithStats.xml       | 1139 +++++++++++++++-
 pbcore/io/FastaIO.py                               |    2 +-
 pbcore/io/align/PacBioBamIndex.py                  |   83 +-
 pbcore/io/dataset/DataSetIO.py                     | 1400 ++++++++++++++------
 pbcore/io/dataset/DataSetMembers.py                |  206 ++-
 pbcore/io/dataset/DataSetReader.py                 |  233 ++--
 pbcore/io/dataset/DataSetValidator.py              |   53 +-
 pbcore/io/dataset/DataSetWriter.py                 |   19 +-
 pbcore/io/dataset/EntryPoints.py                   |   53 +-
 pbcore/util/ToolRunner.py                          |    3 +
 tests/test_pbdataset.py                            |  205 ++-
 tests/test_pbdataset_subtypes.py                   |  174 ++-
 21 files changed, 2996 insertions(+), 687 deletions(-)

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