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afif-guest pushed a commit to branch master
in repository python-pbcore.
commit ddc8b4840390915962e76ccc42217799a469f62a
Merge: 22813b3 0d7b8ea
Author: Afif Elghraoui <a...@ghraoui.name>
Date: Thu Sep 17 18:46:52 2015 -0700
Merge tag 'upstream/1.2.3+dfsg'
Upstream version 1.2.3+dfsg
CHANGELOG.org | 6 +
bin/dataset.py | 3 +
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 +-
76 files changed, 19382 insertions(+), 16091 deletions(-)
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