[med-svn] [nanopolish] branch master updated (7bf0edf -> df599e5)

[Afif Elghraoui]

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afif pushed a change to branch master
in repository nanopolish.

      from  7bf0edf   Merge branch 'master' of git+ssh://anonscm.debian.org:/git/debian-med/nanopolish
       new  97378d1   New upstream version 0.8.4
       new  b9ff356   Merge tag 'upstream/0.8.4'
       new  2a7eb36   Update and refine patches
       new  df599e5   Improve handling of external dependencies and build flags

The 4 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:
 Makefile                                           |     4 +-
 README.md                                          |     2 +-
 debian/patches/compiler-flags.patch                |    17 +-
 debian/patches/dontinstalleigen.patch              |    15 -
 debian/patches/external-dependencies.patch         |    38 +
 debian/patches/external-libs.patch                 |    33 -
 debian/patches/gcc7.patch                          |    15 -
 debian/patches/reproducible.patch                  |     6 +-
 debian/patches/series                              |     6 +-
 debian/patches/write_return_values_ignored.patch   |     8 +-
 debian/rules                                       |    10 +-
 .../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 +-
 76 files changed, 24589 insertions(+), 38067 deletions(-)
 delete mode 100644 debian/patches/dontinstalleigen.patch
 create mode 100644 debian/patches/external-dependencies.patch
 delete mode 100644 debian/patches/external-libs.patch
 delete mode 100644 debian/patches/gcc7.patch
 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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