[med-svn] [pbgenomicconsensus] branch debian/jessie-backports updated (19d44a0 -> 4260e19)

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch debian/jessie-backports
in repository pbgenomicconsensus.

      from  19d44a0   pbgenomicconsensus (1.1.0-1~bpo8+1) jessie-backports; urgency=medium
      adds  da58626   Imported Upstream version 2.0.0+20151210
      adds  71dce52   Merge tag 'upstream/2.0.0+20151210'
      adds  b08aff2   Prepare new revision
      adds  12f1c8d   Update patches
      adds  3fec6fd   Revise debian/*.install file to not be so specific
      adds  b34d90a   Remove manpage for nonexistent script
      adds  3b1f8fe   Add dependency on pbcommand
      adds  5e474ef   Add strict dependency on same version of backend library from same package
      adds  c051dca   Rename manpages to match executables where language extensions dropped upstream
      adds  20b5eba   Add NEWS file to advise users of renamed scripts
      adds  0df2632   Update script names within manpages
      adds  a3306a4   Use secure VCS URLs
      adds  01d537f   Bump copyright year
      adds  041bf6b   pbgenomicconsensus (2.0.0+20151210-1) unstable; urgency=medium
       new  02209fa   Merge tag 'debian/2.0.0+20151210-1' into debian/jessie-backports
       new  4260e19   pbgenomicconsensus (2.0.0+20151210-1~bpo8+1) jessie-backports; urgency=medium

The 2 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
 debian/NEWS                                       |  12 +
 debian/changelog                                  |  21 ++
 debian/control                                    |   9 +-
 debian/copyright                                  |   2 +-
 debian/man/{gffToBed.py.1 => gffToBed.1}          |   4 +-
 debian/man/{gffToVcf.py.1 => gffToVcf.1}          |   4 +-
 debian/man/makePbi.py.1                           |  21 --
 debian/man/summarizeConsensus.1                   |  15 ++
 debian/man/summarizeConsensus.py.1                |  15 --
 debian/patches/manpages.patch                     |  94 +++----
 debian/patches/python-scripts                     |  13 +-
 debian/pbgenomicconsensus.install                 |   8 +-
 debian/rules                                      |   7 +-
 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 +++++++
 49 files changed, 930 insertions(+), 927 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 debian/NEWS
 rename debian/man/{gffToBed.py.1 => gffToBed.1} (65%)
 rename debian/man/{gffToVcf.py.1 => gffToVcf.1} (52%)
 delete mode 100644 debian/man/makePbi.py.1
 create mode 100644 debian/man/summarizeConsensus.1
 delete mode 100644 debian/man/summarizeConsensus.py.1
 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

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbgenomicconsensus.git