[med-svn] [python-pbcore] branch upstream updated (25f1d31 -> 716f5d3)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Aug 4 09:46:57 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch upstream
in repository python-pbcore.
from 25f1d31 Imported Upstream version 1.0.0
adds 716f5d3 Imported Upstream version 1.2.1+dfsg1
No new revisions were added by this update.
Summary of changes:
.circleci/installHDF5.sh | 14 +
.gitignore | 8 +-
CHANGELOG.org | 9 +
LICENSES.txt | 27 +
MANIFEST.in | 15 +
README.md | 18 +-
bin/dataset.py | 62 +
bin/updateXSDs.py | 46 +
circle.yml | 17 +
doc/conf.py | 3 +-
doc/index.rst | 2 +
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.deprecated.rst | 30 -
doc/pbcore.io.dataset.rst | 298 +
pbcore/__init__.py | 2 +-
pbcore/data/Makefile | 37 +
pbcore/data/__init__.py | 9 +-
pbcore/data/aligned_reads_1.bam | Bin 34798 -> 0 bytes
pbcore/data/aligned_reads_1.bam.bai | Bin 160 -> 0 bytes
pbcore/data/bam_mapping.bam | Bin 172060 -> 0 bytes
pbcore/data/bam_mapping.bam.bai | Bin 112 -> 0 bytes
pbcore/data/bam_mapping.bam.pbi | Bin 41344 -> 0 bytes
pbcore/data/cmph5_mapping.cmp.h5 | Bin 236542 -> 0 bytes
pbcore/data/datasets/__init__.py | 58 +
pbcore/data/datasets/alignment.dataset.xml | 48 +
pbcore/data/datasets/barcode.dataset.xml | 11 +
pbcore/data/datasets/ccsread.dataset.xml | 15 +
pbcore/data/datasets/contig.dataset.xml | 18 +
pbcore/data/datasets/fofn.fofn | 2 +
pbcore/data/datasets/hdfsubread_dataset.xml | 72 +
pbcore/data/datasets/lambda.pbalign.xml | 2 +
pbcore/data/datasets/lambda.reference.xml | 2 +
pbcore/data/datasets/pbalchemysim.pbalign.xml | 2 +
pbcore/data/datasets/pbalchemysim0.bas.h5 | Bin 0 -> 437818 bytes
pbcore/data/datasets/pbalchemysim0.pbalign.bam | Bin 0 -> 303745 bytes
pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai | Bin 0 -> 1352 bytes
pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi | Bin 0 -> 2115 bytes
.../pbalchemysim0.pbalign.chunk0contigs.xml | 2 +
.../pbalchemysim0.pbalign.chunk1contigs.xml | 2 +
pbcore/data/datasets/pbalchemysim0.pbalign.xml | 2 +
pbcore/data/datasets/pbalchemysim0.reference.fasta | 1515 ++
.../datasets/pbalchemysim0.reference.fasta.fai | 59 +
pbcore/data/datasets/pbalchemysim0.reference.xml | 2 +
pbcore/data/datasets/pbalchemysim0.subread.xml | 2 +
pbcore/data/datasets/pbalchemysim0.subreads.bam | Bin 0 -> 301012 bytes
pbcore/data/datasets/pbalchemysim1.bas.h5 | Bin 0 -> 420626 bytes
pbcore/data/datasets/pbalchemysim1.pbalign.bam | Bin 0 -> 287718 bytes
pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai | Bin 0 -> 1496 bytes
pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi | Bin 0 -> 2028 bytes
pbcore/data/datasets/pbalchemysim1.pbalign.xml | 2 +
pbcore/data/datasets/pbalchemysim1.subread.xml | 2 +
pbcore/data/datasets/pbalchemysim1.subreads.bam | Bin 0 -> 284875 bytes
pbcore/data/datasets/reference.dataset.xml | 20 +
pbcore/data/datasets/subread.dataset.xml | 472 +
pbcore/data/datasets/subreadSetWithStats.xml | 2 +
.../datasets/transformed_rs_subread.dataset.xml | 72 +
...100569412550000001823090301191423_s1_p0.ccs.bam | Bin 0 -> 280793 bytes
...69412550000001823090301191423_s1_p0.ccs.bam.bai | Bin 0 -> 16 bytes
...00001823085912221377_s1_X0.aligned_subreads.bam | Bin 0 -> 201867 bytes
...1823085912221377_s1_X0.aligned_subreads.bam.bai | Bin 0 -> 112 bytes
...1823085912221377_s1_X0.aligned_subreads.bam.pbi | Bin 0 -> 2521 bytes
...01823085912221377_s1_X0.aligned_subreads.cmp.h5 | Bin 0 -> 297430 bytes
...4852550000001823085912221377_s1_X0.subreads.bam | Bin 202934 -> 204413 bytes
...550000001823085912221377_s1_X0.subreads.bam.bai | Bin 0 -> 16 bytes
...550000001823085912221377_s1_X0.subreads.bam.pbi | Bin 0 -> 1314 bytes
pbcore/io/FastaIO.py | 20 +-
pbcore/io/__init__.py | 2 +
pbcore/io/align/BamAlignment.py | 102 +-
pbcore/io/align/BamIO.py | 70 +-
pbcore/io/align/CmpH5IO.py | 25 +-
pbcore/io/align/PacBioBamIndex.py | 126 +-
pbcore/io/align/_BamSupport.py | 37 +-
pbcore/io/align/__init__.py | 9 +-
pbcore/io/align/_bgzf.py | 860 ++
pbcore/io/base.py | 8 +
pbcore/io/dataset/DataSetIO.py | 2127 +++
pbcore/io/dataset/DataSetMembers.py | 1582 +++
pbcore/io/dataset/DataSetReader.py | 304 +
pbcore/io/dataset/DataSetValidator.py | 53 +
pbcore/io/dataset/DataSetWriter.py | 185 +
pbcore/io/dataset/DataSetXsd.py | 13921 +++++++++++++++++++
pbcore/io/dataset/EntryPoints.py | 170 +
pbcore/io/dataset/__init__.py | 23 +
pbcore/io/opener.py | 77 +-
pbcore/sequence.py | 8 +-
requirements-dev.txt | 3 +
requirements.txt | 4 +
setup.cfg | 2 +
setup.py | 13 +-
tests/test_pbcore_extract_bam_sequence.py | 63 +
tests/test_pbcore_io_AlnFileReaders.py | 329 +-
tests/test_pbcore_io_FastaIO.py | 6 -
tests/test_pbcore_io_lossless_bam.py | 59 +
tests/test_pbcore_io_unaligned_bam.py | 7 +
tests/test_pbcore_util_sequences.py | 12 +-
tests/test_pbdataset.py | 844 ++
tests/test_pbdataset_subtypes.py | 108 +
101 files changed, 23766 insertions(+), 671 deletions(-)
create mode 100644 .circleci/installHDF5.sh
create mode 100644 MANIFEST.in
create mode 100755 bin/dataset.py
create mode 100755 bin/updateXSDs.py
create mode 100644 circle.yml
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
delete mode 100644 doc/pbcore.deprecated.rst
create mode 100644 doc/pbcore.io.dataset.rst
create mode 100644 pbcore/data/Makefile
delete mode 100644 pbcore/data/aligned_reads_1.bam
delete mode 100644 pbcore/data/aligned_reads_1.bam.bai
delete mode 100644 pbcore/data/bam_mapping.bam
delete mode 100644 pbcore/data/bam_mapping.bam.bai
delete mode 100644 pbcore/data/bam_mapping.bam.pbi
delete mode 100644 pbcore/data/cmph5_mapping.cmp.h5
create mode 100755 pbcore/data/datasets/__init__.py
create mode 100644 pbcore/data/datasets/alignment.dataset.xml
create mode 100644 pbcore/data/datasets/barcode.dataset.xml
create mode 100644 pbcore/data/datasets/ccsread.dataset.xml
create mode 100644 pbcore/data/datasets/contig.dataset.xml
create mode 100644 pbcore/data/datasets/fofn.fofn
create mode 100644 pbcore/data/datasets/hdfsubread_dataset.xml
create mode 100644 pbcore/data/datasets/lambda.pbalign.xml
create mode 100644 pbcore/data/datasets/lambda.reference.xml
create mode 100644 pbcore/data/datasets/pbalchemysim.pbalign.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.bas.h5
create mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.bam
create mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai
create mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi
create mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.chunk0contigs.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.chunk1contigs.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.pbalign.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.reference.fasta
create mode 100644 pbcore/data/datasets/pbalchemysim0.reference.fasta.fai
create mode 100644 pbcore/data/datasets/pbalchemysim0.reference.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.subread.xml
create mode 100644 pbcore/data/datasets/pbalchemysim0.subreads.bam
create mode 100644 pbcore/data/datasets/pbalchemysim1.bas.h5
create mode 100644 pbcore/data/datasets/pbalchemysim1.pbalign.bam
create mode 100644 pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai
create mode 100644 pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi
create mode 100644 pbcore/data/datasets/pbalchemysim1.pbalign.xml
create mode 100644 pbcore/data/datasets/pbalchemysim1.subread.xml
create mode 100644 pbcore/data/datasets/pbalchemysim1.subreads.bam
create mode 100644 pbcore/data/datasets/reference.dataset.xml
create mode 100644 pbcore/data/datasets/subread.dataset.xml
create mode 100644 pbcore/data/datasets/subreadSetWithStats.xml
create mode 100644 pbcore/data/datasets/transformed_rs_subread.dataset.xml
create mode 100644 pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam
create mode 100644 pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai
create mode 100644 pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam
create mode 100644 pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai
create mode 100644 pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi
create mode 100644 pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.cmp.h5
create mode 100644 pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.bai
create mode 100644 pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi
create mode 100644 pbcore/io/align/_bgzf.py
create mode 100755 pbcore/io/dataset/DataSetIO.py
create mode 100755 pbcore/io/dataset/DataSetMembers.py
create mode 100755 pbcore/io/dataset/DataSetReader.py
create mode 100755 pbcore/io/dataset/DataSetValidator.py
create mode 100755 pbcore/io/dataset/DataSetWriter.py
create mode 100755 pbcore/io/dataset/DataSetXsd.py
create mode 100755 pbcore/io/dataset/EntryPoints.py
create mode 100755 pbcore/io/dataset/__init__.py
create mode 100644 requirements-dev.txt
create mode 100644 requirements.txt
create mode 100644 setup.cfg
create mode 100644 tests/test_pbcore_extract_bam_sequence.py
create mode 100755 tests/test_pbcore_io_lossless_bam.py
create mode 100644 tests/test_pbdataset.py
create mode 100644 tests/test_pbdataset_subtypes.py
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