[med-svn] [python-pbcore] branch master updated (22813b3 -> f309a92)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Sep 20 08:25:26 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch master
in repository python-pbcore.
from 22813b3 Upload to unstable
new 0d7b8ea Imported Upstream version 1.2.3+dfsg
new ddc8b48 Merge tag 'upstream/1.2.3+dfsg'
new 6c4126a Add patch to skip tests if the necessary scripts can't be found
new 65617fc Install scripts to /usr/bin, but give them sensible names
new 1ff49c1 Rename patch
new c06124a Add dependency on python-pkg-resources for python-pbcore
new 2382c57 Do not rename the script in this patch
new d154b16 Add patches to globally rename dataset.py to pbdataset
new 2e52e9c Override dh_installchangelogs to handle the upstream changelog
new c055b74 Create new changelog entry
new abe64b4 Add manpage stubs directing users to richer documentation sources
new f309a92 Prepare upload
The 12 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 | 6 +
bin/dataset.py | 3 +
debian/README.Debian | 6 +-
debian/changelog | 10 +
debian/control | 3 +-
debian/patches/rename-datasetpy.patch | 179 +
debian/patches/series | 2 +
debian/patches/skip-integration-tests.patch | 46 +
debian/pbdataset.1 | 13 +
debian/pbopen.1 | 13 +
debian/python-pbcore.manpages | 2 +
debian/rules | 10 +-
doc/pacbio-theme/static/headerGradient.jpg | Bin 0 -> 7099 bytes
doc/pacbio-theme/static/pacbio.css | 238 +
doc/pacbio-theme/static/pacbioLogo.png | Bin 0 -> 3128 bytes
doc/pacbio-theme/static/pygments.css | 55 +
doc/pacbio-theme/theme.conf | 4 +
pbcore/__init__.py | 2 +-
pbcore/data/Makefile | 28 +-
pbcore/data/__init__.py | 3 +
pbcore/data/datasets/__init__.py | 20 +-
pbcore/data/datasets/alignment.dataset.xml | 157 +-
pbcore/data/datasets/barcode.dataset.xml | 39 +-
pbcore/data/datasets/ccsaligned.dataset.xml | 48 +
pbcore/data/datasets/ccsread.dataset.xml | 61 +-
pbcore/data/datasets/contig.dataset.xml | 54 +-
pbcore/data/datasets/fofn.fofn | 2 +-
pbcore/data/datasets/lambda.alignmentset.xml | 15 +
pbcore/data/datasets/lambda.pbalign.xml | 2 -
pbcore/data/datasets/lambda.reference.xml | 2 -
pbcore/data/datasets/lambda.referenceset.xml | 19 +
pbcore/data/datasets/pbalchemysim.alignmentset.xml | 57 +
.../data/datasets/pbalchemysim.hdfsubreadset.xml | 11 +
pbcore/data/datasets/pbalchemysim.pbalign.xml | 2 -
.../pbalchemysim0.alignmentset.chunk0contigs.xml | 47 +
.../pbalchemysim0.alignmentset.chunk1contigs.xml | 47 +
.../data/datasets/pbalchemysim0.alignmentset.xml | 15 +
.../data/datasets/pbalchemysim0.hdfsubreadset.xml | 10 +
pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi | Bin 2115 -> 2147 bytes
.../pbalchemysim0.pbalign.chunk0contigs.xml | 2 -
.../pbalchemysim0.pbalign.chunk1contigs.xml | 2 -
pbcore/data/datasets/pbalchemysim0.pbalign.xml | 2 -
pbcore/data/datasets/pbalchemysim0.reference.xml | 77 -
.../data/datasets/pbalchemysim0.referenceset.xml | 77 +
pbcore/data/datasets/pbalchemysim0.subread.xml | 2 -
.../data/datasets/pbalchemysim0.subreads.bam.bai | Bin 0 -> 16 bytes
.../data/datasets/pbalchemysim0.subreads.bam.pbi | Bin 0 -> 1003 bytes
pbcore/data/datasets/pbalchemysim0.subreadset.xml | 10 +
.../data/datasets/pbalchemysim1.alignmentset.xml | 15 +
.../data/datasets/pbalchemysim1.hdfsubreadset.xml | 10 +
pbcore/data/datasets/pbalchemysim1.pbalign.xml | 2 -
pbcore/data/datasets/pbalchemysim1.subread.xml | 2 -
.../data/datasets/pbalchemysim1.subreads.bam.bai | Bin 0 -> 16 bytes
.../data/datasets/pbalchemysim1.subreads.bam.pbi | Bin 0 -> 945 bytes
pbcore/data/datasets/pbalchemysim1.subreadset.xml | 10 +
pbcore/data/datasets/reference.dataset.xml | 69 +-
pbcore/data/datasets/subread.dataset.xml | 1014 +-
pbcore/data/datasets/subreadSetWithStats.xml | 2262 ++-
.../datasets/transformed_rs_subread.dataset.xml | 152 +-
pbcore/data/empty.ccs.bam | Bin 0 -> 540 bytes
pbcore/data/empty.ccs.bam.pbi | Bin 0 -> 67 bytes
pbcore/io/BasH5IO.py | 18 +-
pbcore/io/GffIO.py | 64 +
pbcore/io/align/BamAlignment.py | 29 +-
pbcore/io/align/BamIO.py | 5 +-
pbcore/io/align/PacBioBamIndex.py | 2 +-
pbcore/io/align/_bgzf.py | 55 +-
pbcore/io/dataset/DataSetIO.py | 2898 ++--
pbcore/io/dataset/DataSetMembers.py | 191 +-
pbcore/io/dataset/DataSetReader.py | 100 +-
pbcore/io/dataset/DataSetValidator.py | 2 +
pbcore/io/dataset/DataSetWriter.py | 145 +-
pbcore/io/dataset/DataSetXsd.py | 13884 ++-----------------
pbcore/io/dataset/EntryPoints.py | 63 +-
pbcore/io/dataset/_pbbase.py | 4563 ++++++
pbcore/io/dataset/_pbds.py | 3435 +++++
pbcore/io/dataset/_pbmeta.py | 2056 +++
pbcore/io/dataset/_pbpn.py | 507 +
pbcore/io/dataset/_pbrk.py | 1218 ++
pbcore/io/dataset/_pbsample.py | 632 +
pbcore/io/dataset/utils.py | 125 +
tests/test_pbcore_io_AlnFileReaders.py | 9 +
tests/test_pbcore_io_GffIO.py | 67 +-
tests/test_pbcore_io_bgzf.py | 42 +
tests/test_pbdataset.py | 389 +-
tests/test_pbdataset_subtypes.py | 319 +-
86 files changed, 19657 insertions(+), 16100 deletions(-)
create mode 100644 debian/patches/rename-datasetpy.patch
create mode 100644 debian/patches/skip-integration-tests.patch
create mode 100644 debian/pbdataset.1
create mode 100644 debian/pbopen.1
create mode 100644 debian/python-pbcore.manpages
create mode 100644 doc/pacbio-theme/static/headerGradient.jpg
create mode 100644 doc/pacbio-theme/static/pacbio.css
create mode 100644 doc/pacbio-theme/static/pacbioLogo.png
create mode 100644 doc/pacbio-theme/static/pygments.css
create mode 100644 doc/pacbio-theme/theme.conf
create mode 100644 pbcore/data/datasets/ccsaligned.dataset.xml
create mode 100644 pbcore/data/datasets/lambda.alignmentset.xml
delete mode 100644 pbcore/data/datasets/lambda.pbalign.xml
delete mode 100644 pbcore/data/datasets/lambda.reference.xml
create mode 100644 pbcore/data/datasets/lambda.referenceset.xml
create mode 100644 pbcore/data/datasets/pbalchemysim.alignmentset.xml
create mode 100644 pbcore/data/datasets/pbalchemysim.hdfsubreadset.xml
delete mode 100644 pbcore/data/datasets/pbalchemysim.pbalign.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.alignmentset.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.hdfsubreadset.xml
delete mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.chunk0contigs.xml
delete mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.chunk1contigs.xml
delete mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.xml
delete mode 100644 pbcore/data/datasets/pbalchemysim0.reference.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.referenceset.xml
delete mode 100644 pbcore/data/datasets/pbalchemysim0.subread.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.subreads.bam.bai
create mode 100644 pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi
create mode 100644 pbcore/data/datasets/pbalchemysim0.subreadset.xml
create mode 100644 pbcore/data/datasets/pbalchemysim1.alignmentset.xml
create mode 100644 pbcore/data/datasets/pbalchemysim1.hdfsubreadset.xml
delete mode 100644 pbcore/data/datasets/pbalchemysim1.pbalign.xml
delete mode 100644 pbcore/data/datasets/pbalchemysim1.subread.xml
create mode 100644 pbcore/data/datasets/pbalchemysim1.subreads.bam.bai
create mode 100644 pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi
create mode 100644 pbcore/data/datasets/pbalchemysim1.subreadset.xml
create mode 100644 pbcore/data/empty.ccs.bam
create mode 100644 pbcore/data/empty.ccs.bam.pbi
create mode 100755 pbcore/io/dataset/_pbbase.py
create mode 100755 pbcore/io/dataset/_pbds.py
create mode 100755 pbcore/io/dataset/_pbmeta.py
create mode 100755 pbcore/io/dataset/_pbpn.py
create mode 100755 pbcore/io/dataset/_pbrk.py
create mode 100755 pbcore/io/dataset/_pbsample.py
create mode 100755 pbcore/io/dataset/utils.py
create mode 100644 tests/test_pbcore_io_bgzf.py
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