README.md
setup.py
bin/inStrain
docker/__init__.py
docker/job_utils.py
docker/run_instrain.py
docker/s3_utils.py
inStrain/GeneProfile.py
inStrain/SNVprofile.py
inStrain/__init__.py
inStrain/_version.py
inStrain/argumentParser.py
inStrain/compare_controller.py
inStrain/compare_greedy.py
inStrain/compare_utils.py
inStrain/controller.py
inStrain/filter_reads.py
inStrain/genomeUtilities.py
inStrain/irep_utilities.py
inStrain/logUtils.py
inStrain/quickProfile.py
inStrain/readComparer.py
inStrain/utils.py
inStrain.egg-info/PKG-INFO
inStrain.egg-info/SOURCES.txt
inStrain.egg-info/dependency_links.txt
inStrain.egg-info/not-zip-safe
inStrain.egg-info/requires.txt
inStrain.egg-info/top_level.txt
inStrain/deprecated/DEPRECATEDmapping_plots.py
inStrain/deprecated/__init__.py
inStrain/deprecated/deprecated_filter_reads.py
inStrain/deprecated/deprecated_gene_statistics.py
inStrain/deprecated/plottingUtilities.py
inStrain/helper_files/NullModel.txt
inStrain/plotting/SNV_plots.py
inStrain/plotting/__init__.py
inStrain/plotting/compare_plots.py
inStrain/plotting/gene_plots.py
inStrain/plotting/linkage_plots.py
inStrain/plotting/mapping_plots.py
inStrain/plotting/plotting_controller.py
inStrain/plotting/positional_plots.py
inStrain/plotting/utilities.py
inStrain/profile/__init__.py
inStrain/profile/fasta.py
inStrain/profile/linkage.py
inStrain/profile/profile_controller.py
inStrain/profile/profile_utilities.py
inStrain/profile/samtools_ops.py
inStrain/profile/snv_utilities.py
test/test_suite.py