[med-svn] [nanopolish] 02/04: Merge tag 'upstream/0.8.4'

[Afif Elghraoui]

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commit b9ff356f1ade161006225093a1b36b6045cbec04
Merge: 7bf0edf 97378d1
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Nov 9 22:42:59 2017 -0500

    Merge tag 'upstream/0.8.4'
    
    Upstream version 0.8.4

 Makefile                                           |     4 +-
 README.md                                          |     2 +-
 .../r9.4_70bps.u_to_t_rna.5mer.template.model      |  1031 ++
 scripts/convert_model_to_header.py                 |    27 +-
 scripts/import_ont_model.py                        |    29 +-
 src/alignment/nanopolish_alignment_db.cpp          |    43 +-
 src/alignment/nanopolish_alignment_db.h            |     4 +-
 src/alignment/nanopolish_anchor.cpp                |    16 +-
 src/alignment/nanopolish_anchor.h                  |    52 +-
 src/alignment/nanopolish_eventalign.cpp            |   340 +-
 src/alignment/nanopolish_eventalign.h              |     7 +-
 .../r9_250bps_cpg_6mer_complement_pop1_model.inl   | 15658 -------------------
 .../r9_250bps_cpg_6mer_complement_pop2_model.inl   | 15658 -------------------
 .../r9_250bps_cpg_6mer_template_model.inl          |     9 -
 ...50bps_nucleotide_5mer_complement_pop1_model.inl |     9 -
 ...50bps_nucleotide_5mer_complement_pop2_model.inl |     9 -
 .../r9_250bps_nucleotide_5mer_template_model.inl   |     9 -
 ...50bps_nucleotide_6mer_complement_pop1_model.inl |     9 -
 ...50bps_nucleotide_6mer_complement_pop2_model.inl |     9 -
 .../r9_250bps_nucleotide_6mer_template_model.inl   |     9 -
 .../r9_4_450bps_cpg_6mer_template_model.inl        |     9 -
 .../r9_4_450bps_dam_6mer_template_model.inl        | 15649 ++++++++++++++++++
 ...inl => r9_4_450bps_dcm_6mer_template_model.inl} | 10783 +++++++------
 .../r9_4_450bps_nucleotide_5mer_template_model.inl |     9 -
 .../r9_4_450bps_nucleotide_6mer_template_model.inl |     9 -
 .../r9_4_70bps_u_to_t_rna_5mer_template_model.inl  |  1048 ++
 src/common/logger.hpp                              |     1 +
 src/common/nanopolish_alphabet.cpp                 |    31 +-
 src/common/nanopolish_alphabet.h                   |    34 +-
 src/common/nanopolish_common.h                     |    12 +-
 src/common/nanopolish_variant.cpp                  |    96 +-
 src/common/nanopolish_variant.h                    |    19 +-
 src/hmm/nanopolish_duration_model.cpp              |     2 +-
 src/hmm/nanopolish_emissions.h                     |    83 +-
 src/hmm/nanopolish_hmm_input_sequence.h            |    13 +
 src/hmm/nanopolish_profile_hmm.cpp                 |    30 +-
 src/hmm/nanopolish_profile_hmm.h                   |     3 +
 src/hmm/nanopolish_profile_hmm_r7.cpp              |     4 +-
 src/hmm/nanopolish_profile_hmm_r7.inl              |    14 +-
 src/hmm/nanopolish_profile_hmm_r9.cpp              |     4 +-
 src/hmm/nanopolish_profile_hmm_r9.inl              |     6 +-
 src/hmm/nanopolish_transition_parameters.cpp       |     6 +-
 src/main/nanopolish.cpp                            |     4 +-
 src/nanopolish_call_methylation.cpp                |    18 +-
 src/nanopolish_call_variants.cpp                   |    74 +-
 src/nanopolish_haplotype.cpp                       |     2 +-
 src/nanopolish_index.cpp                           |    13 +-
 src/nanopolish_methyltrain.cpp                     |    66 +-
 src/nanopolish_methyltrain.h                       |     2 +-
 src/nanopolish_raw_loader.cpp                      |   361 +-
 src/nanopolish_raw_loader.h                        |    17 +-
 src/nanopolish_read_db.cpp                         |    51 +-
 src/nanopolish_scorereads.cpp                      |   165 +-
 src/nanopolish_squiggle_read.cpp                   |   339 +-
 src/nanopolish_squiggle_read.h                     |   177 +-
 src/nanopolish_train_poremodel_from_basecalls.cpp  |    13 +-
 .../nanopolish_builtin_models.h                    |     8 +-
 .../nanopolish_model_names.cpp                     |     2 +-
 .../nanopolish_model_names.h                       |     1 +
 .../nanopolish_pore_model_set.cpp                  |    90 +-
 .../nanopolish_pore_model_set.h                    |    36 +-
 src/{ => pore_model}/nanopolish_poremodel.cpp      |    77 +-
 src/{ => pore_model}/nanopolish_poremodel.h        |    39 +-
 src/test/nanopolish_test.cpp                       |   129 +-
 src/thirdparty/scrappie/event_detection.h          |     7 +
 src/training_core.cpp                              |     5 +-
 src/training_core.hpp                              |    13 +-
 67 files changed, 24523 insertions(+), 37985 deletions(-)

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