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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
been added to this reference.
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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