[med-svn] [nanopolish] branch master updated (0035be6 -> 79cea4f)

[Steffen Möller]

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moeller pushed a change to branch master
in repository nanopolish.

      from  0035be6   Added references to registries.
       new  204a942   New upstream version 0.8.1
       new  ed09381   Updated version 0.8.1 from 'upstream/0.8.1'
       new  79cea4f   Proceeded to version 0.8.1

The 3 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                                           |   6 +-
 README.md                                          |  28 +-
 debian/changelog                                   |  12 +
 debian/control                                     |   2 +-
 debian/patches/dontinstalleigen.patch              |  13 +
 debian/patches/fprintf_sizet.patch                 |  26 +
 debian/patches/gcc7.patch                          |  12 +
 debian/patches/series                              |   4 +
 debian/patches/write_return_values_ignored.patch   |  22 +
 debian/rules                                       |   3 +
 scripts/nanopolish_makerange.py                    |  15 +-
 src/alignment/nanopolish_alignment_db.cpp          |  15 +-
 src/alignment/nanopolish_alignment_db.h            |   2 +-
 src/alignment/nanopolish_anchor.cpp                | 223 -----
 src/alignment/nanopolish_anchor.h                  |  15 -
 src/alignment/nanopolish_eventalign.cpp            |  12 +-
 src/common/{fs_support.hpp => fs_support.cpp}      |  28 +-
 src/common/fs_support.hpp                          |  34 +-
 src/common/nanopolish_common.h                     |   2 +-
 src/common/nanopolish_fast5_map.cpp                | 138 ----
 src/common/nanopolish_fast5_map.h                  |  39 -
 src/common/nanopolish_variant.cpp                  |  13 +-
 src/main/nanopolish.cpp                            |   7 +-
 src/nanopolish_call_methylation.cpp                |  12 +-
 src/nanopolish_call_variants.cpp                   |  15 +-
 src/nanopolish_consensus.cpp                       | 897 ---------------------
 src/nanopolish_consensus.h                         |  14 -
 src/nanopolish_extract.cpp                         |  39 +-
 src/nanopolish_getmodel.cpp                        |   4 +-
 src/nanopolish_haplotype.cpp                       |  20 +
 src/nanopolish_haplotype.h                         |   5 +
 src/nanopolish_index.cpp                           | 197 +++++
 ...nanopolish_phase_reads.h => nanopolish_index.h} |  11 +-
 src/nanopolish_methyltrain.cpp                     |  16 +-
 src/nanopolish_phase_reads.cpp                     |  12 +-
 src/nanopolish_raw_loader.cpp                      | 282 +++++++
 src/nanopolish_raw_loader.h                        |  25 +
 src/nanopolish_read_db.cpp                         | 231 ++++++
 src/nanopolish_read_db.h                           |  81 ++
 src/nanopolish_scorereads.cpp                      |   8 +-
 src/nanopolish_squiggle_read.cpp                   | 218 ++++-
 src/nanopolish_squiggle_read.h                     |  34 +-
 src/nanopolish_train_poremodel_from_basecalls.cpp  |   4 +-
 src/test/nanopolish_test.cpp                       |  19 +-
 src/thirdparty/scrappie/event_detection.c          | 319 ++++++++
 src/thirdparty/scrappie/event_detection.h          |  27 +
 src/thirdparty/scrappie/scrappie_common.c          |  73 ++
 src/thirdparty/scrappie/scrappie_common.h          |  10 +
 src/thirdparty/scrappie/scrappie_stdlib.h          |  41 +
 src/thirdparty/scrappie/scrappie_structures.h      |  31 +
 src/thirdparty/scrappie/sse_mathfun.h              | 722 +++++++++++++++++
 src/thirdparty/scrappie/util.c                     | 288 +++++++
 src/thirdparty/scrappie/util.h                     | 197 +++++
 53 files changed, 3038 insertions(+), 1485 deletions(-)
 create mode 100644 debian/patches/dontinstalleigen.patch
 create mode 100644 debian/patches/fprintf_sizet.patch
 create mode 100644 debian/patches/gcc7.patch
 create mode 100644 debian/patches/write_return_values_ignored.patch
 copy src/common/{fs_support.hpp => fs_support.cpp} (67%)
 delete mode 100644 src/common/nanopolish_fast5_map.cpp
 delete mode 100644 src/common/nanopolish_fast5_map.h
 delete mode 100644 src/nanopolish_consensus.cpp
 delete mode 100644 src/nanopolish_consensus.h
 create mode 100644 src/nanopolish_index.cpp
 copy src/{nanopolish_phase_reads.h => nanopolish_index.h} (58%)
 create mode 100644 src/nanopolish_raw_loader.cpp
 create mode 100644 src/nanopolish_raw_loader.h
 create mode 100644 src/nanopolish_read_db.cpp
 create mode 100644 src/nanopolish_read_db.h
 create mode 100644 src/thirdparty/scrappie/event_detection.c
 create mode 100644 src/thirdparty/scrappie/event_detection.h
 create mode 100644 src/thirdparty/scrappie/scrappie_common.c
 create mode 100644 src/thirdparty/scrappie/scrappie_common.h
 create mode 100644 src/thirdparty/scrappie/scrappie_stdlib.h
 create mode 100644 src/thirdparty/scrappie/scrappie_structures.h
 create mode 100644 src/thirdparty/scrappie/sse_mathfun.h
 create mode 100644 src/thirdparty/scrappie/util.c
 create mode 100644 src/thirdparty/scrappie/util.h

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