[med-svn] [python-pbcore] 02/03: Merge tag 'upstream/1.2.4+dfsg'

[Afif Elghraoui]

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

commit 52adfffc48b88942e0a45485d5c96e2187bbf64c
Merge: 3c0a478 a8e05e3
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Oct 26 01:13:45 2015 -0700

    Merge tag 'upstream/1.2.4+dfsg'
    
    Upstream version 1.2.4+dfsg

 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
 ...1823085912221377_s1_X0.subreads.fake_bc.bam.bai | Bin 0 -> 16 bytes
 ...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(-)

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