[med-svn] [python-pbcore] branch master updated (c1fae13 -> 18727af)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Aug 4 09:43:41 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 c1fae13 Upload to experimental due to the python-pysam >=0.8.1 dependency
new 716f5d3 Imported Upstream version 1.2.1+dfsg1
new e7f25e8 Merge tag 'upstream/1.2.1+dfsg1'
new 18727af Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/python-pbcore
The 3 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:
.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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