[med-svn] [nanopolish] 02/03: Updated version 0.8.1 from 'upstream/0.8.1'

[Steffen Möller]

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moeller pushed a commit to branch master
in repository nanopolish.

commit ed093815452bfbf1da4ae1ba347ba49bb9017319
Merge: 0035be6 204a942
Author: Steffen Moeller <moeller at debian.org>
Date:   Thu Sep 14 16:58:50 2017 +0200

    Updated version 0.8.1 from 'upstream/0.8.1'
    
    with Debian dir d6bf28d8c25c748d3588b026a6cd630b9041cd6a

 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 +++++
 src/nanopolish_index.h                            |  14 +
 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, 2953 insertions(+), 1479 deletions(-)

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