[med-svn] [nanopolish] branch upstream updated (204a942 -> 97378d1)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository nanopolish.

      from  204a942   New upstream version 0.8.1
       new  97378d1   New upstream version 0.8.4

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
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Summary of changes:
 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(-)
 create mode 100644 etc/r9-models/r9.4_70bps.u_to_t_rna.5mer.template.model
 delete mode 100644 src/builtin_models/r9_250bps_cpg_6mer_complement_pop1_model.inl
 delete mode 100644 src/builtin_models/r9_250bps_cpg_6mer_complement_pop2_model.inl
 create mode 100644 src/builtin_models/r9_4_450bps_dam_6mer_template_model.inl
 copy src/builtin_models/{r9_4_450bps_cpg_6mer_template_model.inl => r9_4_450bps_dcm_6mer_template_model.inl} (67%)
 create mode 100644 src/builtin_models/r9_4_70bps_u_to_t_rna_5mer_template_model.inl
 rename src/{hmm => pore_model}/nanopolish_builtin_models.h (83%)
 rename src/{common => pore_model}/nanopolish_model_names.cpp (97%)
 rename src/{common => pore_model}/nanopolish_model_names.h (98%)
 rename src/{hmm => pore_model}/nanopolish_pore_model_set.cpp (55%)
 rename src/{hmm => pore_model}/nanopolish_pore_model_set.h (64%)
 rename src/{ => pore_model}/nanopolish_poremodel.cpp (74%)
 rename src/{ => pore_model}/nanopolish_poremodel.h (73%)

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