[med-svn] [nanopolish] branch debian/jessie-backports updated (624896a -> be60119)

[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 nanopolish.

      from  624896a   nanopolish (0.4.0-1~bpo8+1) jessie-backports; urgency=medium
      adds  6df3241   fix FTBFS in GCC6
      adds  6ad75ac   enable full hardening
      adds  3b4df74   fix Vcs-*
      adds  354fdae   bump Standards-Version
      adds  28a56e7   dch -r
      adds  af726c2   make build reproducible
      adds  aa2ebdb   Imported Upstream version 0.5.0
      adds  7786888   Merge tag 'upstream/0.5.0'
      adds  364b82d   Refresh and update patches
      adds  eec93cb   Update email address and copyright year
      adds  25cbfab   Add build dependency on libeigen3
      adds  932dff5   Fix "clean" target
      adds  9accad7   Fix compatibility with fast5 0.5.6
      adds  3570b45   releasing package nanopolish version 0.5.0-1
       new  248728f   Merge tag 'debian/0.5.0-1' into debian/jessie-backports
       new  be60119   releasing package nanopolish version 0.5.0-1~bpo8+1

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:
 .gitignore                                        |    5 +
 Makefile                                          |   15 +-
 README.md                                         |   35 +-
 debian/changelog                                  |   35 +
 debian/control                                    |   10 +-
 debian/copyright                                  |    4 +-
 debian/patches/adjust-include-path.patch          |  141 +-
 debian/patches/compiler-flags.patch               |   17 +-
 debian/patches/external-libs.patch                |   16 +
 debian/patches/fast5-0.5.6.patch                  |   33 +
 debian/patches/fix-ftbfs-with-gcc6.patch          |   14 +
 debian/patches/reproducible.patch                 |   17 +
 debian/patches/series                             |    3 +
 debian/rules                                      |    3 +-
 etc/r9-models/nanopolish_models.fofn              |    2 +
 etc/r9-models/template_median68pA.5mers.model     | 1030 ++++++
 etc/r9-models/template_median68pA.model           | 4101 +++++++++++++++++++++
 scripts/consensus.make                            |    8 +-
 scripts/dropmodel.py                              |   73 +
 scripts/nanopolish_makerange.py                   |   13 +-
 scripts/nanopolish_merge.py                       |   50 +-
 src/alignment/nanopolish_alignment_db.cpp         |  158 +-
 src/alignment/nanopolish_alignment_db.h           |   15 +-
 src/alignment/nanopolish_anchor.cpp               |   64 +-
 src/alignment/nanopolish_anchor.h                 |    5 +-
 src/alignment/nanopolish_eventalign.cpp           |  158 +-
 src/alignment/nanopolish_eventalign.h             |    2 +-
 src/common/logger.hpp                             |  260 ++
 src/common/logsum.cpp                             |    3 +
 src/common/logsumset.hpp                          |   80 +
 src/common/nanopolish_alphabet.cpp                |  125 +-
 src/common/nanopolish_alphabet.h                  |  363 +-
 src/common/nanopolish_common.cpp                  |   28 +
 src/common/nanopolish_common.h                    |   18 +-
 src/common/nanopolish_fast5_map.cpp               |    4 +-
 src/common/nanopolish_iupac.h                     |    2 +-
 src/common/nanopolish_model_names.cpp             |   66 +
 src/common/nanopolish_model_names.h               |   41 +
 src/common/nanopolish_variant.cpp                 |  257 +-
 src/common/nanopolish_variant.h                   |   26 +-
 src/common/progress.h                             |   12 +-
 src/hmm/invgauss.hpp                              |  149 +
 src/hmm/nanopolish_duration_model.cpp             |   90 +
 src/hmm/nanopolish_duration_model.h               |   57 +
 src/hmm/nanopolish_emissions.h                    |   92 +-
 src/hmm/nanopolish_hmm_input_sequence.h           |   10 +-
 src/hmm/nanopolish_pore_model_set.cpp             |  100 +
 src/hmm/nanopolish_pore_model_set.h               |   72 +
 src/hmm/nanopolish_profile_hmm.cpp                |   94 +-
 src/hmm/nanopolish_profile_hmm.h                  |   36 +-
 src/hmm/nanopolish_profile_hmm.inl                |  185 +-
 src/hmm/nanopolish_transition_parameters.cpp      |  200 +-
 src/hmm/nanopolish_transition_parameters.h        |   12 +-
 src/main/nanopolish.cpp                           |   66 +-
 src/nanopolish_call_variants.cpp                  |  697 +++-
 src/nanopolish_call_variants.h                    |    2 +-
 src/nanopolish_consensus.cpp                      |   92 +-
 src/nanopolish_consensus.h                        |    2 +-
 src/nanopolish_getmodel.cpp                       |    1 +
 src/nanopolish_getmodel.h                         |    2 +-
 src/nanopolish_haplotype.cpp                      |   36 +-
 src/nanopolish_haplotype.h                        |   27 +-
 src/nanopolish_methyltest.cpp                     |  155 +-
 src/nanopolish_methyltrain.cpp                    |  859 +++--
 src/nanopolish_methyltrain.h                      |   25 +-
 src/nanopolish_poremodel.cpp                      |  214 +-
 src/nanopolish_poremodel.h                        |   59 +-
 src/nanopolish_scorereads.cpp                     |  593 +++
 src/nanopolish_scorereads.h                       |   32 +
 src/nanopolish_squiggle_read.cpp                  |  418 ++-
 src/nanopolish_squiggle_read.h                    |  106 +-
 src/nanopolish_train_poremodel_from_basecalls.cpp |  398 ++
 src/nanopolish_train_poremodel_from_basecalls.h   |   15 +
 src/test/nanopolish_test.cpp                      |  416 ++-
 src/training_core.cpp                             |  265 ++
 src/training_core.hpp                             |  176 +
 76 files changed, 11571 insertions(+), 1494 deletions(-)
 create mode 100644 debian/patches/fast5-0.5.6.patch
 create mode 100644 debian/patches/fix-ftbfs-with-gcc6.patch
 create mode 100644 debian/patches/reproducible.patch
 create mode 100644 etc/r9-models/nanopolish_models.fofn
 create mode 100644 etc/r9-models/template_median68pA.5mers.model
 create mode 100644 etc/r9-models/template_median68pA.model
 create mode 100644 scripts/dropmodel.py
 create mode 100644 src/common/logger.hpp
 create mode 100644 src/common/logsumset.hpp
 create mode 100644 src/common/nanopolish_model_names.cpp
 create mode 100644 src/common/nanopolish_model_names.h
 create mode 100644 src/hmm/invgauss.hpp
 create mode 100755 src/hmm/nanopolish_duration_model.cpp
 create mode 100755 src/hmm/nanopolish_duration_model.h
 create mode 100644 src/hmm/nanopolish_pore_model_set.cpp
 create mode 100644 src/hmm/nanopolish_pore_model_set.h
 create mode 100644 src/nanopolish_scorereads.cpp
 create mode 100644 src/nanopolish_scorereads.h
 create mode 100644 src/nanopolish_train_poremodel_from_basecalls.cpp
 create mode 100644 src/nanopolish_train_poremodel_from_basecalls.h
 create mode 100644 src/training_core.cpp
 create mode 100644 src/training_core.hpp

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