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commit e7f25e8d830f3a7df9b00b021e5be5d9271a6426 Merge: b0130e0 716f5d3 Author: Afif Elghraoui <[email protected]> Date: Mon Aug 3 23:36:26 2015 -0700 Merge tag 'upstream/1.2.1+dfsg1' Upstream version 1.2.1+dfsg1 .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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
