.travis.yml
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README.rst
install.sh
requirements.txt
setup.cfg
setup.py
tests.sh
tests_fast.sh
upload_pypi.sh
RNFtools.egg-info/PKG-INFO
RNFtools.egg-info/SOURCES.txt
RNFtools.egg-info/dependency_links.txt
RNFtools.egg-info/not-zip-safe
RNFtools.egg-info/pbr.json
RNFtools.egg-info/requires.txt
RNFtools.egg-info/top_level.txt
bin/rnf-join-fq.py
docs/Makefile
docs/conf.py
docs/developers.rst
docs/faq.rst
docs/first_steps.rst
docs/index.rst
docs/installation.rst
docs/introduction.rst
docs/lavender.rst
docs/make.bat
docs/mishmash.rst
docs/other_tools.rst
docs/rnf.rst
examples/.gitignore
examples/01_simple_read_simulation/Snakefile
examples/02_more_complex_read_simulation/Snakefile
examples/03_mapper_evaluation_SE/Snakefile
examples/03_mapper_evaluation_SE/bams/Snakefile
examples/04_mapper_evaluation_PE/Snakefile
examples/04_mapper_evaluation_PE/bams/Snakefile
rnftools/__init__.py
rnftools/errors.py
rnftools/include_all.snake
rnftools/lavender/__init__.py
rnftools/lavender/bam.py
rnftools/lavender/lavender.snake
rnftools/lavender/panel.py
rnftools/lavender/report.py
rnftools/mishmash/__init__.py
rnftools/mishmash/artIllumina.py
rnftools/mishmash/cuReSim.py
rnftools/mishmash/dwgSim.py
rnftools/mishmash/mishmash.snake
rnftools/mishmash/sample.py
rnftools/mishmash/source.py
rnftools/mishmash/wgSim.py
rnftools/rnfformat/__init__.py
rnftools/rnfformat/formatter.py
rnftools/rnfformat/read.py
rnftools/rnfformat/segment.py