[med-svn] [python-cutadapt] branch upstream updated (9b0e316 -> 500335b)
Andreas Tille
tille at debian.org
Sat Feb 10 12:31:44 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository python-cutadapt.
from 9b0e316 New upstream version 1.13
new 500335b New upstream version 1.15
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
been added to this reference.
Summary of changes:
CHANGES.rst | 35 +-
MANIFEST.in | 14 +-
PKG-INFO | 2 +-
cutadapt.egg-info/entry_points.txt | 3 -
cutadapt.egg-info/requires.txt | 1 -
cutadapt/scripts/__init__.py | 0
doc/conf.py | 6 +-
doc/develop.rst | 124 +
doc/guide.rst | 289 +-
doc/ideas.rst | 16 +-
doc/index.rst | 1 +
doc/installation.rst | 69 +-
doc/recipes.rst | 86 +
setup.cfg | 4 +-
setup.py | 45 +-
.../cutadapt.egg-info}/PKG-INFO | 2 +-
.../cutadapt.egg-info}/SOURCES.txt | 81 +-
.../cutadapt.egg-info}/dependency_links.txt | 0
src/cutadapt.egg-info/entry_points.txt | 3 +
src/cutadapt.egg-info/requires.txt | 1 +
.../cutadapt.egg-info}/top_level.txt | 0
{cutadapt => src/cutadapt}/__init__.py | 0
.../cutadapt.py => src/cutadapt/__main__.py | 674 +--
{cutadapt => src/cutadapt}/_align.c | 1580 ++---
{cutadapt => src/cutadapt}/_align.pyx | 5 +
{cutadapt => src/cutadapt}/_qualtrim.c | 266 +-
{cutadapt => src/cutadapt}/_qualtrim.pyx | 0
{cutadapt => src/cutadapt}/_seqio.c | 6265 ++++++++++++++------
{cutadapt => src/cutadapt}/_seqio.pyx | 98 +
{cutadapt => src/cutadapt}/_version.py | 4 +-
{cutadapt => src/cutadapt}/adapters.py | 165 +-
{cutadapt => src/cutadapt}/align.py | 0
{cutadapt => src/cutadapt}/colorspace.py | 0
{cutadapt => src/cutadapt}/compat.py | 0
{cutadapt => src/cutadapt}/filters.py | 183 +-
{cutadapt => src/cutadapt}/modifiers.py | 61 +-
src/cutadapt/pipeline.py | 651 ++
{cutadapt => src/cutadapt}/qualtrim.py | 0
{cutadapt => src/cutadapt}/report.py | 254 +-
{cutadapt => src/cutadapt}/seqio.py | 226 +-
tests/cut/demultiplexed.first.1.fastq | 4 +
tests/cut/demultiplexed.first.2.fastq | 4 +
tests/cut/demultiplexed.second.1.fastq | 4 +
...-short.2.fastq => demultiplexed.second.2.fastq} | 0
...d-m27.1.fastq => demultiplexed.unknown.1.fastq} | 8 -
...immed.2.fastq => demultiplexed.unknown.2.fastq} | 4 +
...d-not-anchored.fasta => linked-discard-g.fasta} | 6 -
tests/cut/linked-discard.fasta | 6 +
tests/cut/linked-not-anchored.fasta | 4 +-
tests/data/block1.fastq.bz2 | Bin 87 -> 0 bytes
tests/data/block2.fastq.bz2 | Bin 206 -> 0 bytes
tests/{testadapters.py => test_adapters.py} | 76 +-
tests/{testalign.py => test_align.py} | 0
tests/{testcolorspace.py => test_colorspace.py} | 4 +-
tests/{tests.py => test_commandline.py} | 52 +-
tests/{testfilters.py => test_filters.py} | 9 +-
tests/{testmodifiers.py => test_modifiers.py} | 0
tests/{testpaired.py => test_paired.py} | 257 +-
tests/{testqualtrim.py => test_qualtrim.py} | 1 +
tests/{testseqio.py => test_seqio.py} | 81 +-
tests/test_trim.py | 57 +
tests/testtrim.py | 28 -
tests/utils.py | 28 +-
63 files changed, 7680 insertions(+), 4167 deletions(-)
delete mode 100644 cutadapt.egg-info/entry_points.txt
delete mode 100644 cutadapt.egg-info/requires.txt
delete mode 100644 cutadapt/scripts/__init__.py
create mode 100644 doc/develop.rst
rename {cutadapt.egg-info => src/cutadapt.egg-info}/PKG-INFO (99%)
rename {cutadapt.egg-info => src/cutadapt.egg-info}/SOURCES.txt (78%)
rename {cutadapt.egg-info => src/cutadapt.egg-info}/dependency_links.txt (100%)
create mode 100644 src/cutadapt.egg-info/entry_points.txt
create mode 100644 src/cutadapt.egg-info/requires.txt
rename {cutadapt.egg-info => src/cutadapt.egg-info}/top_level.txt (100%)
rename {cutadapt => src/cutadapt}/__init__.py (100%)
rename cutadapt/scripts/cutadapt.py => src/cutadapt/__main__.py (63%)
rename {cutadapt => src/cutadapt}/_align.c (88%)
rename {cutadapt => src/cutadapt}/_align.pyx (99%)
rename {cutadapt => src/cutadapt}/_qualtrim.c (94%)
rename {cutadapt => src/cutadapt}/_qualtrim.pyx (100%)
rename {cutadapt => src/cutadapt}/_seqio.c (59%)
rename {cutadapt => src/cutadapt}/_seqio.pyx (64%)
rename {cutadapt => src/cutadapt}/_version.py (82%)
rename {cutadapt => src/cutadapt}/adapters.py (83%)
rename {cutadapt => src/cutadapt}/align.py (100%)
rename {cutadapt => src/cutadapt}/colorspace.py (100%)
rename {cutadapt => src/cutadapt}/compat.py (100%)
rename {cutadapt => src/cutadapt}/filters.py (57%)
rename {cutadapt => src/cutadapt}/modifiers.py (78%)
create mode 100644 src/cutadapt/pipeline.py
rename {cutadapt => src/cutadapt}/qualtrim.py (100%)
rename {cutadapt => src/cutadapt}/report.py (50%)
rename {cutadapt => src/cutadapt}/seqio.py (80%)
create mode 100644 tests/cut/demultiplexed.first.1.fastq
create mode 100644 tests/cut/demultiplexed.first.2.fastq
create mode 100644 tests/cut/demultiplexed.second.1.fastq
copy tests/cut/{paired-too-short.2.fastq => demultiplexed.second.2.fastq} (100%)
copy tests/cut/{paired-m27.1.fastq => demultiplexed.unknown.1.fastq} (52%)
copy tests/cut/{paired-untrimmed.2.fastq => demultiplexed.unknown.2.fastq} (62%)
copy tests/cut/{linked-not-anchored.fasta => linked-discard-g.fasta} (57%)
create mode 100644 tests/cut/linked-discard.fasta
delete mode 100644 tests/data/block1.fastq.bz2
delete mode 100644 tests/data/block2.fastq.bz2
rename tests/{testadapters.py => test_adapters.py} (59%)
rename tests/{testalign.py => test_align.py} (100%)
rename tests/{testcolorspace.py => test_colorspace.py} (98%)
rename tests/{tests.py => test_commandline.py} (91%)
rename tests/{testfilters.py => test_filters.py} (80%)
rename tests/{testmodifiers.py => test_modifiers.py} (100%)
rename tests/{testpaired.py => test_paired.py} (56%)
rename tests/{testqualtrim.py => test_qualtrim.py} (99%)
rename tests/{testseqio.py => test_seqio.py} (75%)
create mode 100644 tests/test_trim.py
delete mode 100644 tests/testtrim.py
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