[med-svn] [python-pbcore] branch master updated (6592b8b -> 0bf210c)

[Afif Elghraoui]

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

      from  6592b8b   python-pbcore (1.2.7+dfsg-2) unstable; urgency=medium
       new  60c0774   Imported Upstream version 1.2.9+dfsg
       new  8ae588d   Merge tag 'upstream/1.2.9+dfsg'
       new  75d0a45   Prepare new revision
       new  76efaf4   Refresh patches
       new  5ec2cc7   Mark patch as forwarded and slightly modify it
       new  092ab67   Add patch to prevent installation of relocated script
       new  ae6b96b   Update d/control style
       new  dafa8d9   Add new tests dependency on python-pyxb
       new  2423b55   Remove handling for pbdataset script
       new  011d2d6   Add NEWS file to warn users about the missing pbdataset script
       new  800358e   Make corrections to the pbopen manpage
       new  0bf210c   releasing package python-pbcore version 1.2.9+dfsg-1

The 12 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 CHANGELOG.org                                      |   14 +-
 bin/dataset.py                                     |   64 +-
 debian/NEWS                                        |    7 +
 debian/changelog                                   |   11 +
 debian/control                                     |   37 +-
 debian/patches/deprecate-dataset.patch             |   14 +
 debian/patches/pysam-0.9.0.patch                   |   13 +-
 debian/patches/remove-unnecessary-cython-dep.patch |    2 +-
 debian/patches/series                              |    1 +
 debian/pbdataset.1                                 |   13 -
 debian/pbopen.1                                    |   16 +-
 debian/python-pbcore.manpages                      |    1 -
 debian/rules                                       |    2 -
 debian/tests/control                               |    5 +-
 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 ++++-
 43 files changed, 2889 insertions(+), 1311 deletions(-)
 create mode 100644 debian/NEWS
 create mode 100644 debian/patches/deprecate-dataset.patch
 delete mode 100644 debian/pbdataset.1
 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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