[med-svn] [python-pbcore] branch upstream updated (b924872 -> 60c0774)

[Afif Elghraoui]

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

      from  b924872   Imported Upstream version 1.2.7+dfsg
       new  60c0774   Imported Upstream version 1.2.9+dfsg

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 CHANGELOG.org                                      |   14 +-
 bin/dataset.py                                     |   64 +-
 doc/pbcore.io.rst                                  |   24 +-
 pbcore/__init__.py                                 |    2 +-
 pbcore/chemistry/resources/mapping.xml             |    8 +-
 pbcore/data/datasets/__init__.py                   |    6 +-
 pbcore/data/datasets/empty_lambda.aligned.bam      |  Bin 0 -> 700 bytes
 pbcore/data/datasets/empty_lambda.aligned.bam.bai  |  Bin 0 -> 24 bytes
 pbcore/data/datasets/empty_lambda.aligned.bam.pbi  |  Bin 0 -> 67 bytes
 ...69412550000001823090301191423_s1_p0.ccs.bam.pbi |  Bin 0 -> 297 bytes
 pbcore/io/BasH5IO.py                               |  145 +--
 pbcore/io/FastaIO.py                               |   20 +-
 pbcore/io/align/BamAlignment.py                    |   45 +-
 pbcore/io/align/BamIO.py                           |   45 +-
 pbcore/io/align/CmpH5IO.py                         |   99 +-
 pbcore/io/align/_BamSupport.py                     |    7 +-
 pbcore/io/dataset/DataSetIO.py                     | 1272 +++++++++++++-------
 pbcore/io/dataset/DataSetMembers.py                |  338 ++++--
 pbcore/io/dataset/DataSetReader.py                 |   49 +-
 pbcore/io/dataset/DataSetWriter.py                 |   10 +
 pbcore/io/dataset/EntryPoints.py                   |  246 ----
 pbcore/io/dataset/utils.py                         |   20 +-
 pbcore/io/rangeQueries.py                          |    4 +-
 pbcore/model/__init__.py                           |    2 +
 pbcore/model/baseRegions.py                        |  192 +++
 requirements-dev.txt                               |    1 +
 requirements.txt                                   |    2 +-
 tests/test_pbcore_io_BasH5Reader.py                |    3 +-
 tests/test_pbcore_io_unaligned_bam.py              |    2 +-
 tests/test_pbdataset.py                            | 1139 ++++++++++++++++--
 tests/test_pbdataset_subtypes.py                   |  319 ++++-
 31 files changed, 2810 insertions(+), 1268 deletions(-)
 create mode 100644 pbcore/data/datasets/empty_lambda.aligned.bam
 create mode 100644 pbcore/data/datasets/empty_lambda.aligned.bam.bai
 create mode 100644 pbcore/data/datasets/empty_lambda.aligned.bam.pbi
 create mode 100644 pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi
 delete mode 100755 pbcore/io/dataset/EntryPoints.py
 create mode 100644 pbcore/model/baseRegions.py

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