[med-svn] [nanopolish] 05/09: Merge tag 'upstream/0.8.5'

[Afif Elghraoui]

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afif pushed a commit to branch master
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commit 1b9384f5e36350e01d81b9965e812ae756f4788e
Merge: 649786e 436609f
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Feb 4 16:05:34 2018 -0500

    Merge tag 'upstream/0.8.5'
    
    Upstream version 0.8.5

 Makefile                                           |  26 +-
 README.md                                          |  11 +-
 docs/Makefile                                      |  20 +
 docs/source/_static/nanopolish-workflow.png        | Bin 0 -> 318184 bytes
 .../_static/quickstart_methylation_results.png     | Bin 0 -> 50765 bytes
 docs/source/conf.py                                | 168 +++++++++
 docs/source/debug.rst                              | 170 +++++++++
 docs/source/index.rst                              |  30 ++
 docs/source/installation.rst                       |  45 +++
 docs/source/manual.rst                             | 413 +++++++++++++++++++++
 docs/source/quickstart_call_methylation.rst        | 125 +++++++
 docs/source/quickstart_consensus.rst               | 115 ++++++
 docs/source/quickstart_eventalign.rst              | 103 +++++
 scripts/calculate_methylation_frequency.py         |  11 +-
 scripts/extract_reads_aligned_to_region.py         | 309 +++++++++++++++
 scripts/nanopolish_merge.py                        |  17 +-
 src/alignment/nanopolish_alignment_db.cpp          |   1 +
 src/alignment/nanopolish_eventalign.cpp            | 134 ++-----
 src/common/nanopolish_bam_processor.cpp            |   3 +-
 src/common/nanopolish_common.h                     |   2 +-
 src/main/nanopolish.cpp                            |   9 +-
 src/nanopolish_call_variants.cpp                   |   6 +-
 src/nanopolish_extract.cpp                         |  70 ++--
 src/nanopolish_index.cpp                           |  18 +-
 src/nanopolish_raw_loader.cpp                      |  12 +-
 src/nanopolish_read_db.cpp                         |  19 +-
 src/nanopolish_squiggle_read.cpp                   |  46 ++-
 27 files changed, 1703 insertions(+), 180 deletions(-)

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