[med-svn] [python-pbcore] 02/04: Merge tag 'upstream/1.2.11+dfsg'

[Afif Elghraoui]

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

commit c63a73c4f4a671fd4093a0745f09d214fa50eb10
Merge: 620c3bb 114e570
Author: Afif Elghraoui <afif at debian.org>
Date:   Wed Jan 25 22:49:34 2017 -0800

    Merge tag 'upstream/1.2.11+dfsg'
    
    Upstream version 1.2.11+dfsg

 .circleci/installHDF5.sh                           |    2 +-
 CHANGELOG.org                                      |    5 +
 Makefile                                           |    5 +
 pbcore/__init__.py                                 |    2 +-
 pbcore/chemistry/resources/mapping.xml             |   60 +-
 pbcore/data/__init__.py                            |    3 +
 pbcore/data/empty.aligned_subreads.bam             |  Bin 0 -> 728 bytes
 pbcore/data/empty.aligned_subreads.bam.pbi         |  Bin 0 -> 67 bytes
 pbcore/io/GffIO.py                                 |   70 +-
 pbcore/io/align/BamIO.py                           |   26 +-
 pbcore/io/align/CmpH5IO.py                         |    6 +-
 pbcore/io/align/PacBioBamIndex.py                  |   10 +-
 pbcore/io/dataset/DataSetErrors.py                 |   34 +
 pbcore/io/dataset/DataSetIO.py                     |  339 +++---
 pbcore/io/dataset/DataSetMembers.py                |  850 +++++++++------
 pbcore/io/dataset/DataSetMetaTypes.py              |   86 ++
 pbcore/io/dataset/DataSetReader.py                 |   46 +-
 pbcore/{__init__.py => io/dataset/DataSetUtils.py} |   61 +-
 pbcore/io/dataset/DataSetValidator.py              |   41 +-
 pbcore/io/dataset/DataSetWriter.py                 |   43 +-
 pbcore/io/dataset/__init__.py                      |   35 +
 pbcore/io/dataset/utils.py                         |  172 ++-
 requirements-dev.txt                               |    2 +-
 tests/test_pbcore_io_AlnFileReaders.py             |   12 +-
 tests/test_pbcore_io_GffIO.py                      |   11 +
 tests/test_pbdataset.py                            | 1090 ++++----------------
 tests/test_pbdataset_filters.py                    |  373 +++++++
 tests/test_pbdataset_metadata.py                   |  114 ++
 tests/test_pbdataset_split.py                      |  506 +++++++++
 tests/test_pbdataset_subtypes.py                   |  205 ++--
 tests/test_pbdataset_utils.py                      |  183 ++++
 tests/utils.py                                     |   40 +
 32 files changed, 2842 insertions(+), 1590 deletions(-)

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