[med-svn] [nanopolish] branch upstream updated (97378d1 -> 436609f)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository nanopolish.

      from  97378d1   New upstream version 0.8.4
       new  436609f   New upstream version 0.8.5

The 1 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
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Summary of changes:
 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(-)
 create mode 100644 docs/Makefile
 create mode 100644 docs/source/_static/nanopolish-workflow.png
 create mode 100644 docs/source/_static/quickstart_methylation_results.png
 create mode 100644 docs/source/conf.py
 create mode 100644 docs/source/debug.rst
 create mode 100644 docs/source/index.rst
 create mode 100644 docs/source/installation.rst
 create mode 100644 docs/source/manual.rst
 create mode 100644 docs/source/quickstart_call_methylation.rst
 create mode 100644 docs/source/quickstart_consensus.rst
 create mode 100644 docs/source/quickstart_eventalign.rst
 mode change 100644 => 100755 scripts/calculate_methylation_frequency.py
 create mode 100755 scripts/extract_reads_aligned_to_region.py

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