[med-svn] [pbgenomicconsensus] 01/02: Merge tag 'debian/2.0.0+20151210-1' into debian/jessie-backports

[Afif Elghraoui]

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

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

commit 02209fa55ba48d9dde2f7c2582044e681ea83ad7
Merge: 19d44a0 041bf6b
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Tue Mar 15 21:21:05 2016 -0700

    Merge tag 'debian/2.0.0+20151210-1' into debian/jessie-backports

 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                                  |  15 ++
 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, 924 insertions(+), 927 deletions(-)

diff --cc debian/changelog
index 8611365,66050a6..0d80388
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,18 +1,24 @@@
+ pbgenomicconsensus (2.0.0+20151210-1) unstable; urgency=medium
+ 
+   * Imported Upstream version 2.0.0+20151210
+     (corresponds to upstream release tag "smrtanalysis-3.0.2")
+   * Update patches
+   * Revise debian/*.install file to not be so specific
+   * Remove manpage for nonexistent script
+   * Add dependency on pbcommand
+   * Add strict dependency on same version of backend library from same package
+   * Rename manpages to match executables where language extensions dropped upstream
+   * Add NEWS file to advise users of renamed scripts
+   * Use secure VCS URLs in debian/control
+ 
+  -- Afif Elghraoui <afif at ghraoui.name>  Fri, 12 Feb 2016 00:47:38 -0800
+ 
 +pbgenomicconsensus (1.1.0-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Afif Elghraoui <afif at ghraoui.name>  Mon, 07 Dec 2015 21:45:20 -0800
 +
  pbgenomicconsensus (1.1.0-1) unstable; urgency=medium
  
    * Imported Upstream version 1.1.0 (untagged release: bee9a1f from Jun 24)

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