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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
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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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