[med-svn] [nanopolish] branch upstream updated (7f34bba -> 204a942)

[Steffen Möller]

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moeller pushed a change to branch upstream
in repository nanopolish.

      from  7f34bba   New upstream version 0.7.2
      adds  204a942   New upstream version 0.8.1

No new revisions were added by this update.

Summary of changes:
 Makefile                                           |   6 +-
 README.md                                          |  28 +-
 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 +++++
 45 files changed, 2945 insertions(+), 1484 deletions(-)
 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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