This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository python-pbcore.
commit 52adfffc48b88942e0a45485d5c96e2187bbf64c Merge: 3c0a478 a8e05e3 Author: Afif Elghraoui <[email protected]> Date: Mon Oct 26 01:13:45 2015 -0700 Merge tag 'upstream/1.2.4+dfsg' Upstream version 1.2.4+dfsg CHANGELOG.org | 4 + 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.io.dataset.rst | 95 ++++++- pbcore/__init__.py | 2 +- pbcore/data/datasets/__init__.py | 3 + ...00001823085912221377_s1_X0.subreads.fake_bc.bam | Bin 0 -> 192565 bytes ...1823085912221377_s1_X0.subreads.fake_bc.bam.bai | Bin 0 -> 16 bytes ...1823085912221377_s1_X0.subreads.fake_bc.bam.pbi | Bin 0 -> 1523 bytes pbcore/data/datasets/pbalchemysim0.pbalign.bam | Bin 303745 -> 303947 bytes pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi | Bin 2147 -> 2159 bytes pbcore/data/datasets/pbalchemysim0.subreads.bam | Bin 301012 -> 301048 bytes .../data/datasets/pbalchemysim0.subreads.bam.pbi | Bin 1003 -> 1030 bytes pbcore/data/datasets/pbalchemysim1.pbalign.bam | Bin 287718 -> 287902 bytes pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi | Bin 2028 -> 2082 bytes pbcore/data/datasets/pbalchemysim1.subreads.bam | Bin 284875 -> 284903 bytes .../data/datasets/pbalchemysim1.subreads.bam.pbi | Bin 945 -> 965 bytes pbcore/data/empty.ccs.bam | Bin 540 -> 507 bytes pbcore/data/empty.ccs.bam.pbi | Bin 67 -> 67 bytes ...100569412550000001823090301191423_s1_p0.ccs.bam | Bin 280793 -> 278396 bytes ...00001823085912221377_s1_X0.aligned_subreads.bam | Bin 201867 -> 201960 bytes ...1823085912221377_s1_X0.aligned_subreads.bam.bai | Bin 112 -> 112 bytes ...1823085912221377_s1_X0.aligned_subreads.bam.pbi | Bin 2521 -> 2609 bytes ...564852550000001823085912221377_s1_X0.scraps.bam | Bin 0 -> 608536 bytes ...4852550000001823085912221377_s1_X0.subreads.bam | Bin 204413 -> 204543 bytes ...550000001823085912221377_s1_X0.subreads.bam.pbi | Bin 1314 -> 1463 bytes pbcore/io/BasH5IO.py | 9 + pbcore/io/FastaIO.py | 2 + pbcore/io/GffIO.py | 97 +++++-- pbcore/io/align/BamAlignment.py | 4 +- pbcore/io/align/BamIO.py | 12 +- pbcore/io/align/PacBioBamIndex.py | 43 ++- pbcore/io/dataset/DataSetIO.py | 306 ++++++++++++++++----- pbcore/io/dataset/DataSetMembers.py | 73 +++-- pbcore/io/dataset/DataSetReader.py | 1 + pbcore/io/dataset/DataSetValidator.py | 30 +- pbcore/io/dataset/DataSetWriter.py | 21 +- pbcore/io/dataset/EntryPoints.py | 38 ++- pbcore/io/dataset/_pbds.py | 2 +- pbcore/io/dataset/utils.py | 79 ++++-- tests/test_pbcore_extract_bam_sequence.py | 4 +- tests/test_pbcore_io_AlnFileReaders.py | 39 ++- tests/test_pbcore_io_GffIO.py | 27 +- tests/test_pbdataset.py | 185 +++++++++++-- tests/test_pbdataset_subtypes.py | 82 +++++- 48 files changed, 921 insertions(+), 534 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
