[med-svn] [nanopolish] branch master updated (6927949 -> 9cfaa6b)

[Afif Elghraoui]

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afif pushed a change to branch master
in repository nanopolish.

      from  6927949   releasing package nanopolish version 0.8.4-1
       new  a3f03f0   d/control: add sse-support to Build-Depends for i386
       new  1ca3539   d/control: Remove explicit declaration of x32
       new  649786e   Bump Standards-Version to 4.1.3
       new  436609f   New upstream version 0.8.5
       new  1b9384f   Merge tag 'upstream/0.8.5'
       new  4a135b3   Drop patches applied upstream
       new  14d3d48   Drop useless patch
       new  3e2a379   Bump copyright years
       new  9cfaa6b   releasing package nanopolish version 0.8.5-1

The 9 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 +-
 debian/changelog                                   |  13 +
 debian/control                                     |   5 +-
 debian/copyright                                   |   4 +-
 debian/patches/compiler-flags.patch                |  27 --
 debian/patches/external-dependencies.patch         |  38 --
 debian/patches/series                              |   3 -
 debian/patches/write_return_values_ignored.patch   |  24 --
 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 ++-
 34 files changed, 1721 insertions(+), 276 deletions(-)
 delete mode 100644 debian/patches/compiler-flags.patch
 delete mode 100644 debian/patches/external-dependencies.patch
 delete mode 100644 debian/patches/write_return_values_ignored.patch
 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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