[med-svn] [pbgenomicconsensus] 02/03: Merge tag 'upstream/2.0.0+20151210'

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository pbgenomicconsensus.

commit 71dce5212fb7b0028ad501b78c2ef83384bafc1c
Merge: 43f2095 da58626
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Feb 3 00:51:30 2016 -0800

    Merge tag 'upstream/2.0.0+20151210'
    
    Upstream version 2.0.0+20151210

 GenomicConsensus/ResultCollector.py               |   6 +-
 GenomicConsensus/Worker.py                        |   2 +-
 GenomicConsensus/consensus.py                     |   6 +-
 GenomicConsensus/io/utils.py                      |   3 +-
 GenomicConsensus/main.py                          | 121 ++++++---
 GenomicConsensus/options.py                       | 145 +++++++----
 GenomicConsensus/plurality/plurality.py           |   2 +-
 GenomicConsensus/quiver/model.py                  |   2 +-
 GenomicConsensus/quiver/quiver.py                 |   7 +-
 GenomicConsensus/quiver/utils.py                  |   2 +-
 GenomicConsensus/reference.py                     |  53 ++--
 GenomicConsensus/utils.py                         |  61 ++++-
 README.md                                         |  24 +-
 bin/gffToBed                                      | 209 ++++++++++++++++
 bin/gffToBed.py                                   | 141 -----------
 bin/{gffToVcf.py => gffToVcf}                     |  94 +++++--
 bin/makePbi.py                                    | 115 ---------
 bin/plurality                                     |   2 +-
 bin/quiver                                        |   2 +-
 bin/{summarizeConsensus.py => summarizeConsensus} | 114 +++++++--
 bin/{variantCaller.py => variantCaller}           |   0
 doc/HowToQuiver.rst                               |  79 +++---
 setup.py                                          |  15 +-
 tests/cram/bad_input.t                            |   5 +
 tests/cram/extra/convert-to-bed.t                 |   4 +-
 tests/cram/extra/convert-to-vcf.t                 |   2 +-
 tests/cram/extra/coverage-bed.t                   |   4 +-
 tests/cram/extra/plurality-compressed.t           |   2 +-
 tests/cram/extra/plurality-fluidigm.t             |   2 +-
 tests/cram/internal/alignment_summary.t           |   4 +-
 tests/cram/internal/quiver-compatibility.t        |   4 +-
 tests/cram/internal/quiver-staph.t                |  21 +-
 tests/cram/makePbi.t.off                          | 284 ----------------------
 tests/cram/plurality-hcv.t                        |   2 +-
 tests/cram/version.t                              |  11 +-
 tests/unit/test_tool_contract.py                  |  82 +++++++
 36 files changed, 829 insertions(+), 803 deletions(-)

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