[med-svn] [python-pbcore] branch upstream updated (0d7b8ea -> a8e05e3)

[Afif Elghraoui]

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

      from  0d7b8ea   Imported Upstream version 1.2.3+dfsg
       new  a8e05e3   Imported Upstream version 1.2.4+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
been added to this reference.


Summary of changes:
 CHANGELOG.org                                      |   4 +
 doc/pacbio-theme/static/headerGradient.jpg         | Bin 7099 -> 0 bytes
 doc/pacbio-theme/static/pacbio.css                 | 238 ----------------
 doc/pacbio-theme/static/pacbioLogo.png             | Bin 3128 -> 0 bytes
 doc/pacbio-theme/static/pygments.css               |  55 ----
 doc/pacbio-theme/theme.conf                        |   4 -
 doc/pbcore.io.dataset.rst                          |  95 ++++++-
 pbcore/__init__.py                                 |   2 +-
 pbcore/data/datasets/__init__.py                   |   3 +
 ...00001823085912221377_s1_X0.subreads.fake_bc.bam | Bin 0 -> 192565 bytes
 ...823085912221377_s1_X0.subreads.fake_bc.bam.bai} | Bin
 ...1823085912221377_s1_X0.subreads.fake_bc.bam.pbi | Bin 0 -> 1523 bytes
 pbcore/data/datasets/pbalchemysim0.pbalign.bam     | Bin 303745 -> 303947 bytes
 pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi | Bin 2147 -> 2159 bytes
 pbcore/data/datasets/pbalchemysim0.subreads.bam    | Bin 301012 -> 301048 bytes
 .../data/datasets/pbalchemysim0.subreads.bam.pbi   | Bin 1003 -> 1030 bytes
 pbcore/data/datasets/pbalchemysim1.pbalign.bam     | Bin 287718 -> 287902 bytes
 pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi | Bin 2028 -> 2082 bytes
 pbcore/data/datasets/pbalchemysim1.subreads.bam    | Bin 284875 -> 284903 bytes
 .../data/datasets/pbalchemysim1.subreads.bam.pbi   | Bin 945 -> 965 bytes
 pbcore/data/empty.ccs.bam                          | Bin 540 -> 507 bytes
 pbcore/data/empty.ccs.bam.pbi                      | Bin 67 -> 67 bytes
 ...100569412550000001823090301191423_s1_p0.ccs.bam | Bin 280793 -> 278396 bytes
 ...00001823085912221377_s1_X0.aligned_subreads.bam | Bin 201867 -> 201960 bytes
 ...1823085912221377_s1_X0.aligned_subreads.bam.bai | Bin 112 -> 112 bytes
 ...1823085912221377_s1_X0.aligned_subreads.bam.pbi | Bin 2521 -> 2609 bytes
 ...564852550000001823085912221377_s1_X0.scraps.bam | Bin 0 -> 608536 bytes
 ...4852550000001823085912221377_s1_X0.subreads.bam | Bin 204413 -> 204543 bytes
 ...550000001823085912221377_s1_X0.subreads.bam.pbi | Bin 1314 -> 1463 bytes
 pbcore/io/BasH5IO.py                               |   9 +
 pbcore/io/FastaIO.py                               |   2 +
 pbcore/io/GffIO.py                                 |  97 +++++--
 pbcore/io/align/BamAlignment.py                    |   4 +-
 pbcore/io/align/BamIO.py                           |  12 +-
 pbcore/io/align/PacBioBamIndex.py                  |  43 ++-
 pbcore/io/dataset/DataSetIO.py                     | 306 ++++++++++++++++-----
 pbcore/io/dataset/DataSetMembers.py                |  73 +++--
 pbcore/io/dataset/DataSetReader.py                 |   1 +
 pbcore/io/dataset/DataSetValidator.py              |  30 +-
 pbcore/io/dataset/DataSetWriter.py                 |  21 +-
 pbcore/io/dataset/EntryPoints.py                   |  38 ++-
 pbcore/io/dataset/_pbds.py                         |   2 +-
 pbcore/io/dataset/utils.py                         |  79 ++++--
 tests/test_pbcore_extract_bam_sequence.py          |   4 +-
 tests/test_pbcore_io_AlnFileReaders.py             |  39 ++-
 tests/test_pbcore_io_GffIO.py                      |  27 +-
 tests/test_pbdataset.py                            | 185 +++++++++++--
 tests/test_pbdataset_subtypes.py                   |  82 +++++-
 48 files changed, 921 insertions(+), 534 deletions(-)
 delete mode 100644 doc/pacbio-theme/static/headerGradient.jpg
 delete mode 100644 doc/pacbio-theme/static/pacbio.css
 delete mode 100644 doc/pacbio-theme/static/pacbioLogo.png
 delete mode 100644 doc/pacbio-theme/static/pygments.css
 delete mode 100644 doc/pacbio-theme/theme.conf
 create mode 100644 pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam
 copy pbcore/data/{m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.bai => datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai} (100%)
 create mode 100644 pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi
 create mode 100644 pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam

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