[med-svn] [nanopolish] branch master updated (af726c2 -> 3570b45)

[Afif Elghraoui]

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

afif pushed a change to branch master
in repository nanopolish.

      from  af726c2   make build reproducible
       new  aa2ebdb   Imported Upstream version 0.5.0
       new  7786888   Merge tag 'upstream/0.5.0'
       new  364b82d   Refresh and update patches
       new  eec93cb   Update email address and copyright year
       new  25cbfab   Add build dependency on libeigen3
       new  932dff5   Fix "clean" target
       new  9accad7   Fix compatibility with fast5 0.5.6
       new  3570b45   releasing package nanopolish version 0.5.0-1

The 8 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                                  |   11 +
 debian/control                                    |    4 +-
 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          |    6 +-
 debian/patches/reproducible.patch                 |    6 +-
 debian/patches/series                             |    1 +
 debian/rules                                      |    2 +-
 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, 11516 insertions(+), 1497 deletions(-)
 create mode 100644 debian/patches/fast5-0.5.6.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