[med-svn] [pbgenomicconsensus] branch master updated (43f2095 -> b08aff2)

[Afif Elghraoui]

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

      from  43f2095   pbgenomicconsensus (1.1.0-1) unstable; urgency=medium
       new  da58626   Imported Upstream version 2.0.0+20151210
       new  71dce52   Merge tag 'upstream/2.0.0+20151210'
       new  b08aff2   Prepare new revision

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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
 debian/changelog                                  |   6 +
 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 +++++++
 37 files changed, 835 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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