.travis.yml
LICENSE
README.rst
install.sh
requirements.txt
setup.cfg
setup.py
upload_pypi.sh
RNFtools.egg-info/PKG-INFO
RNFtools.egg-info/SOURCES.txt
RNFtools.egg-info/dependency_links.txt
RNFtools.egg-info/entry_points.txt
RNFtools.egg-info/not-zip-safe
RNFtools.egg-info/pbr.json
RNFtools.egg-info/requires.txt
RNFtools.egg-info/top_level.txt
docs/Makefile
docs/conf.py
docs/getting_started.rst
docs/index.rst
docs/make.bat
docs/other_information.rst
docs/reference.rst
docs/tutorial.rst
docs/other_information/01_faq.rst
docs/other_information/02_developers.rst
docs/other_information/03_read_simulators.rst
docs/reference/01_mishmash.rst
docs/reference/02_lavender.rst
docs/reference/03_rnf_format.rst
docs/reference/04_command_line.rst
docs/reference/command_line/art2rnf.txt
docs/reference/command_line/check.txt
docs/reference/command_line/curesim2rnf.txt
docs/reference/command_line/dwgsim2rnf.txt
docs/reference/command_line/es2et.txt
docs/reference/command_line/et2roc.txt
docs/reference/command_line/main.txt
docs/reference/command_line/mason2rnf.txt
docs/reference/command_line/merge.txt
docs/reference/command_line/publication.txt
docs/reference/command_line/sam2es.txt
docs/reference/command_line/sam2rnf.txt
docs/reference/command_line/sam2roc.txt
docs/reference/command_line/save_help.sh
docs/reference/command_line/wgsim2rnf.txt
docs/tutorial/00_installation.rst
docs/tutorial/01_first_snakefile.rst
docs/tutorial/02_simulation.rst
docs/tutorial/03_evaluation.rst
docs/tutorial/05_extending_rnf.rst
examples/.gitignore
examples/01_tutorial/01_first_snakefile/Snakefile
examples/01_tutorial/01_first_snakefile/run.sh
examples/01_tutorial/02_simulation/01_simple_simulation/Snakefile
examples/01_tutorial/02_simulation/01_simple_simulation/run.sh
examples/01_tutorial/02_simulation/02_paired_end_reads/Snakefile
examples/01_tutorial/02_simulation/02_paired_end_reads/run.sh
examples/01_tutorial/02_simulation/03_different_simulator/Snakefile
examples/01_tutorial/02_simulation/03_different_simulator/run.sh
examples/01_tutorial/02_simulation/04_more_genomes/Snakefile
examples/01_tutorial/02_simulation/04_more_genomes/run.sh
examples/01_tutorial/02_simulation/05_more_samples/Snakefile
examples/01_tutorial/02_simulation/05_more_samples/run.sh
examples/01_tutorial/02_simulation/06_nonstandard_parameters/Snakefile
examples/01_tutorial/02_simulation/06_nonstandard_parameters/run.sh
examples/01_tutorial/03_evaluation/01_simple_evaluation/run.sh
examples/01_tutorial/03_evaluation/01_simple_evaluation/bams/Snakefile
examples/01_tutorial/03_evaluation/01_simple_evaluation/report/Snakefile
examples/01_tutorial/03_evaluation/02_single_end/run.sh
examples/01_tutorial/03_evaluation/02_single_end/bams/Snakefile
examples/01_tutorial/03_evaluation/02_single_end/report/Snakefile
examples/01_tutorial/03_evaluation/03_paired_end/run.sh
examples/01_tutorial/03_evaluation/03_paired_end/bams/Snakefile
examples/01_tutorial/03_evaluation/03_paired_end/report/Snakefile
examples/02_all_simulators_example/Snakefile
examples/02_all_simulators_example/run.sh
examples/03_rnf_paper_example/run.sh
examples/03_rnf_paper_example/bams/Snakefile
examples/03_rnf_paper_example/report/Snakefile
rnftools/__init__.py
rnftools/include_all.snake
rnftools/scripts.py
rnftools/lavender/Bam.py
rnftools/lavender/Panel.py
rnftools/lavender/Report.py
rnftools/lavender/__init__.py
rnftools/lavender/lavender.snake
rnftools/mishmash/ArtIllumina.py
rnftools/mishmash/CuReSim.py
rnftools/mishmash/DwgSim.py
rnftools/mishmash/FaiIndex.py
rnftools/mishmash/MasonIllumina.py
rnftools/mishmash/Sample.py
rnftools/mishmash/Source.py
rnftools/mishmash/WgSim.py
rnftools/mishmash/__init__.py
rnftools/mishmash/mishmash.snake
rnftools/rnfformat/Formatter.py
rnftools/rnfformat/FqCreator.py
rnftools/rnfformat/FqMerger.py
rnftools/rnfformat/ReadTuple.py
rnftools/rnfformat/Segment.py
rnftools/rnfformat/__init__.py
tests/.gitignore
tests/tests_clean.sh
tests/tests_install_bats.sh
tests/tests_run.sh
tests/command_line/.gitignore
tests/command_line/__ensure_programs.snake
tests/command_line/humanmito.fa
tests/command_line/humanmito.fa.fai
tests/command_line/rnf_alignment.bam
tests/command_line/rnf_alignment.es
tests/command_line/rnf_alignment.et
tests/command_line/rnf_alignment.sam
tests/command_line/rnf_fq_pe_1.fq
tests/command_line/rnf_fq_pe_2.fq
tests/command_line/rnf_fq_se_1.fq
tests/command_line/rnf_fq_se_2.fq
tests/command_line/rnftools_art2rnf.sh
tests/command_line/rnftools_check.sh
tests/command_line/rnftools_curesim2rnf.sh
tests/command_line/rnftools_dwgsim2rnf.sh
tests/command_line/rnftools_es2et.sh
tests/command_line/rnftools_et2roc.sh
tests/command_line/rnftools_mason2rnf.sh
tests/command_line/rnftools_merge.sh
tests/command_line/rnftools_publication.sh
tests/command_line/rnftools_sam2es.sh
tests/command_line/rnftools_sam2roc.sh
tests/command_line/rnftools_wgsim2rnf.sh
tests/snakemake/01_SE_simulation/Snakefile
tests/snakemake/01_SE_simulation/run.sh
tests/snakemake/02_PE_simulation/Snakefile
tests/snakemake/02_PE_simulation/run.sh