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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
been added to this reference.
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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