[med-svn] [python-pbcore] branch upstream updated (114e570 -> 4a2399d)

[Afif Elghraoui]

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

      from  114e570   Imported Upstream version 1.2.11+dfsg
       new  4a2399d   New upstream version 1.4.2+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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Summary of changes:
 .pylintrc                                          |   15 +
 CHANGELOG.org                                      |    8 +
 Makefile                                           |    6 +-
 README.md                                          |   12 +
 bamboo_build.sh                                    |   23 +
 bin/dataset.py                                     |   13 -
 bin/updateXSDs.py                                  |   18 +-
 pbcore/__init__.py                                 |    2 +-
 pbcore/chemistry/chemistry.py                      |    9 +-
 pbcore/chemistry/resources/mapping.xml             |  170 +-
 pbcore/data/__init__.py                            |    3 +
 pbcore/data/chemistry.xml                          |    9 +
 pbcore/data/datasets/hdfsubread_dataset.xml        |    9 +-
 pbcore/data/datasets/subread.dataset.xml           |   25 +-
 .../datasets/transformed_rs_subread.dataset.xml    |   16 +-
 pbcore/io/BarcodeH5Reader.py                       |   22 +-
 pbcore/io/BasH5IO.py                               |   16 +-
 pbcore/io/VcfIO.py                                 |  179 ++
 pbcore/io/__init__.py                              |    1 +
 pbcore/io/_utils.py                                |   12 +-
 pbcore/io/align/BamIO.py                           |    7 +-
 pbcore/io/align/CmpH5IO.py                         |   10 +-
 pbcore/io/dataset/DataSetIO.py                     |  649 ++++--
 pbcore/io/dataset/DataSetMembers.py                |  720 ++++---
 pbcore/io/dataset/DataSetReader.py                 |   60 +-
 pbcore/io/dataset/DataSetValidator.py              |    7 +-
 pbcore/io/dataset/DataSetWriter.py                 |  111 +-
 pbcore/io/dataset/pyxb/DataSetXsd.py               | 2148 ++++++++++++++++++++
 pbcore/io/dataset/pyxb/__init__.py                 |    0
 pbcore/io/dataset/{ => pyxb}/_pbbase.py            | 1983 +++++++++++-------
 pbcore/io/dataset/{DataSetXsd.py => pyxb/_pbds.py} |  908 +++++----
 pbcore/io/dataset/{ => pyxb}/_pbmeta.py            | 1087 ++++++----
 pbcore/io/dataset/pyxb/_pbpn.py                    |  941 +++++++++
 pbcore/io/dataset/{ => pyxb}/_pbrk.py              |  414 ++--
 pbcore/io/dataset/{ => pyxb}/_pbsample.py          |  318 +--
 pbcore/io/dataset/utils.py                         |  321 +--
 pbcore/io/opener.py                                |    2 +-
 pbcore/io/rangeQueries.py                          |   17 +-
 pbcore/util/__init__.py                            |    4 +
 requirements-dev.txt                               |    4 +-
 requirements.txt                                   |    1 -
 setup.py                                           |    2 +-
 tests/test_pbcore_extract_bam_sequence.py          |    5 +-
 tests/test_pbcore_io_AlnFileReaders.py             |   23 +-
 tests/test_pbcore_io_VcfIO.py                      |   64 +
 tests/test_pbcore_io_lossless_bam.py               |    5 +-
 tests/test_pbdataset.py                            |  577 +++++-
 tests/test_pbdataset_filters.py                    |  274 ++-
 tests/test_pbdataset_metadata.py                   |   59 +-
 tests/test_pbdataset_split.py                      |  348 +++-
 tests/test_pbdataset_subtypes.py                   |  108 +-
 tests/test_pbdataset_utils.py                      |   75 +-
 tests/utils.py                                     |   22 +-
 53 files changed, 8943 insertions(+), 2899 deletions(-)
 create mode 100644 .pylintrc
 create mode 100755 bamboo_build.sh
 delete mode 100755 bin/dataset.py
 create mode 100644 pbcore/data/chemistry.xml
 create mode 100644 pbcore/io/VcfIO.py
 create mode 100644 pbcore/io/dataset/pyxb/DataSetXsd.py
 create mode 100644 pbcore/io/dataset/pyxb/__init__.py
 rename pbcore/io/dataset/{ => pyxb}/_pbbase.py (72%)
 rename pbcore/io/dataset/{DataSetXsd.py => pyxb/_pbds.py} (81%)
 rename pbcore/io/dataset/{ => pyxb}/_pbmeta.py (61%)
 create mode 100644 pbcore/io/dataset/pyxb/_pbpn.py
 rename pbcore/io/dataset/{ => pyxb}/_pbrk.py (74%)
 rename pbcore/io/dataset/{ => pyxb}/_pbsample.py (62%)
 create mode 100644 tests/test_pbcore_io_VcfIO.py

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