[med-svn] [pbgenomicconsensus] branch upstream updated (2e74dad -> da58626)

[Afif Elghraoui]

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afif-guest pushed a change to branch upstream
in repository pbgenomicconsensus.

      from  2e74dad   Imported Upstream version 1.1.0
       new  da58626   Imported Upstream version 2.0.0+20151210

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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(-)
 create mode 100755 bin/gffToBed
 delete mode 100755 bin/gffToBed.py
 rename bin/{gffToVcf.py => gffToVcf} (58%)
 delete mode 100755 bin/makePbi.py
 rename bin/{summarizeConsensus.py => summarizeConsensus} (52%)
 rename bin/{variantCaller.py => variantCaller} (100%)
 create mode 100644 tests/cram/bad_input.t
 delete mode 100644 tests/cram/makePbi.t.off
 create mode 100644 tests/unit/test_tool_contract.py

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