[med-svn] [nanopolish] 02/08: Merge tag 'upstream/0.5.0'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository nanopolish.

commit 77868887d33c651c96e3976b8341cb7c964fa31f
Merge: af726c2 aa2ebdb
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Aug 11 19:55:14 2016 -0700

    Merge tag 'upstream/0.5.0'
    
    Upstream version 0.5.0

 .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(-)

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