[med-svn] [nanopolish] branch upstream updated (cd31d65 -> aa2ebdb)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository nanopolish.

      from  cd31d65   Imported Upstream version 0.4.0
       new  aa2ebdb   Imported Upstream version 0.5.0

The 1 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 +-
 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 +
 65 files changed, 11421 insertions(+), 1351 deletions(-)
 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

-- 
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