[med-svn] [pbalign] 02/08: Merge tag 'upstream/0.3.0'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository pbalign.

commit 32216481a649fb1f43622f740e9b46a36bab8c31
Merge: e37cb3e e530517
Author: Afif Elghraoui <afif at debian.org>
Date:   Fri Dec 23 17:14:06 2016 -0800

    Merge tag 'upstream/0.3.0'
    
    Upstream version 0.3.0

 LICENSES.txt                                      |  34 +-
 Makefile                                          |  11 +-
 README.md                                         |  18 +-
 doc/howto.rst                                     |   7 +-
 pbalign/__init__.py                               |   4 +-
 pbalign/alignservice/align.py                     |   6 +-
 pbalign/alignservice/blasr.py                     | 105 ++++--
 pbalign/bampostservice.py                         | 137 +++++++
 pbalign/ccs.py                                    |  32 ++
 pbalign/filterservice.py                          |  33 +-
 pbalign/forquiverservice/__init__.py              |  34 --
 pbalign/forquiverservice/forquiver.py             |  99 -----
 pbalign/forquiverservice/loadchemistry.py         |  77 ----
 pbalign/forquiverservice/loadpulses.py            | 103 ------
 pbalign/forquiverservice/repack.py                |  87 -----
 pbalign/forquiverservice/sort.py                  |  89 -----
 pbalign/options.py                                | 416 ++++++++++++++--------
 pbalign/pbalignfiles.py                           |  41 ++-
 pbalign/pbalignrunner.py                          | 247 ++++++-------
 pbalign/tasks/__init__.py                         |   0
 pbalign/tasks/consolidate_alignments.py           |  96 +++++
 pbalign/tools/createChemistryHeader.py            |   4 +-
 pbalign/utils/fileutil.py                         |  35 +-
 pbalign/utils/progutil.py                         |   2 +-
 setup.py                                          |   6 +-
 tests/cram/bam.t                                  |  14 +
 tests/cram/ccs.t                                  |  15 +
 tests/cram/dataset_tiny.t                         |  38 ++
 tests/cram/filtercriteria_hitpolicy.t             |  78 ++++
 tests/cram/path_with_space.t                      |   9 +
 tests/cram/setup.sh                               |  21 ++
 tests/cram/test_pbalign.t                         | 276 --------------
 tests/cram/xml.t                                  |  38 ++
 tests/cram_h5/ccs.t                               |  51 +++
 tests/cram_h5/filter_adapter_only.t               |  11 +
 tests/cram_h5/inputs_outputs.t                    | 130 +++++++
 tests/cram_h5/pulsefile.t                         |  23 ++
 tests/cram_h5/setup.sh                            |  22 ++
 tests/{cram => cram_h5}/test_mask_aligned_reads.t |   2 +-
 tests/data/1.config                               |   3 +-
 tests/data/ecoli_lp.fofn                          |   4 +-
 tests/data/lambda_bax.fofn                        |   2 +-
 tests/data/reference_lambda.xml                   |  14 +
 tests/data/subreads_dataset1.xml                  |  21 ++
 tests/data/subreads_dataset2.xml                  |  10 +
 tests/data/test_bas.fofn                          |   2 +-
 tests/data/test_ccs.fofn                          |   2 +-
 tests/data/test_filterAdapterOnly.fofn            |   2 +-
 tests/data/test_leftmost_query.fasta              |   2 +-
 tests/data/test_pulseFile.fofn                    |   8 +-
 tests/out/readme                                  |   3 +-
 tests/unit/nose.cfg                               |  17 +
 tests/unit/test_fileutil.py                       |  63 ++--
 tests/unit/test_options.py                        | 109 +++---
 tests/unit/test_pbalign.py                        |  37 +-
 tests/unit/test_pbalignfiles.py                   |  31 +-
 tests/unit/test_referenceInfo.py                  |   3 +-
 tests/unit/test_setpath.py                        |  25 ++
 tests/unit/test_tool_contract.py                  |  91 +++++
 tests/unit/test_unrolled.py                       |  87 +++++
 tests/unit/test_xmlout.py                         |  38 ++
 tests/unit_h5/nose.cfg                            |  17 +
 tests/{unit => unit_h5}/test_filterservice.py     |  11 +-
 tests/{unit => unit_h5}/test_forquiverservice.py  |  11 +-
 tests/{unit => unit_h5}/test_gmap.py              |   8 +-
 tests/{unit => unit_h5}/test_loadpulsesservice.py |   8 +-
 tests/{unit => unit_h5}/test_pbalign.py           |  11 +-
 tests/{unit => unit_h5}/test_repackservice.py     |   7 +-
 tests/{unit => unit_h5}/test_rgnh5io.py           |  10 +-
 tests/unit_h5/test_setpath.py                     |  27 ++
 tests/{unit => unit_h5}/test_sortservice.py       |   5 +-
 71 files changed, 1837 insertions(+), 1303 deletions(-)

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