[med-svn] [python-pbcore] branch master updated (0bf210c -> 620c3bb)

[Afif Elghraoui]

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

      from  0bf210c   releasing package python-pbcore version 1.2.9+dfsg-1
       new  a06a1f0   Imported Upstream version 1.2.10+dfsg
       new  06db5ad   Merge tag 'upstream/1.2.10+dfsg'
       new  a454197   Drop patch applied upstream
       new  b51022d   Don't raise exception if pyxb version does not exactly match
       new  8d32cb4   Bump Standards-Version to 3.9.8
       new  620c3bb   releasing package python-pbcore version 1.2.10+dfsg-1

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repository and will be described in separate emails.  The revisions
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Summary of changes:
 CHANGELOG.org                                      |   5 +
 debian/changelog                                   |  10 +
 debian/control                                     |   2 +-
 debian/patches/ignore-pyxb.patch                   |  88 ++++++
 debian/patches/pysam-0.9.0.patch                   |  27 --
 debian/patches/remove-unnecessary-cython-dep.patch |   2 +-
 debian/patches/series                              |   2 +-
 pbcore/__init__.py                                 |   2 +-
 pbcore/chemistry/resources/mapping.xml             |  71 ++++-
 pbcore/io/align/BamAlignment.py                    |   2 +-
 pbcore/io/align/PacBioBamIndex.py                  |  17 +
 pbcore/io/dataset/DataSetErrors.py                 |  17 +
 pbcore/io/dataset/DataSetIO.py                     | 313 +++++++++++++-----
 pbcore/io/dataset/DataSetMembers.py                | 185 +++++++----
 pbcore/io/dataset/DataSetReader.py                 |  44 ++-
 pbcore/io/dataset/utils.py                         |  81 ++++-
 requirements.txt                                   |   2 +-
 tests/test_pbcore_io_AlnFileReaders.py             |  19 ++
 tests/test_pbdataset.py                            | 348 ++++++++++++++++++++-
 tests/test_pbdataset_subtypes.py                   | 129 +++++++-
 20 files changed, 1174 insertions(+), 192 deletions(-)
 create mode 100644 debian/patches/ignore-pyxb.patch
 delete mode 100644 debian/patches/pysam-0.9.0.patch
 create mode 100644 pbcore/io/dataset/DataSetErrors.py

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