MANIFEST.in
README.md
setup.py
cassiopeia/__init__.py
cassiopeia/__main__.py
cassiopeia/ProcessingPipeline/__init__.py
cassiopeia/ProcessingPipeline/process/__init__.py
cassiopeia/ProcessingPipeline/process/bam10X2fastq.pl
cassiopeia/ProcessingPipeline/process/callAlleles-PCT-Dian.pl
cassiopeia/ProcessingPipeline/process/callAlleles-PCT17.pl
cassiopeia/ProcessingPipeline/process/callAlleles-PCT48.pl
cassiopeia/ProcessingPipeline/process/changeCellBCID.py
cassiopeia/ProcessingPipeline/process/collapse.py
cassiopeia/ProcessingPipeline/process/collapseBam2dataFrame.pl
cassiopeia/ProcessingPipeline/process/collapseDF2fastq.pl
cassiopeia/ProcessingPipeline/process/collapseFastq_UMI.py
cassiopeia/ProcessingPipeline/process/collapseUMIReadsByMSALargeFile.py
cassiopeia/ProcessingPipeline/process/collapse_cython.c
cassiopeia/ProcessingPipeline/process/collapse_cython.pyx
cassiopeia/ProcessingPipeline/process/consensusTable2fasta.pl
cassiopeia/ProcessingPipeline/process/extractBarcodes.pl
cassiopeia/ProcessingPipeline/process/filterMoleculeTables.py
cassiopeia/ProcessingPipeline/process/lineageGroup.py
cassiopeia/ProcessingPipeline/process/lineageGroup_utils.c
cassiopeia/ProcessingPipeline/process/lineageGroup_utils.pyx
cassiopeia/ProcessingPipeline/process/pickSeq.py
cassiopeia/ProcessingPipeline/process/pipeline_utils.py
cassiopeia/ProcessingPipeline/process/processBam2MT.pl
cassiopeia/ProcessingPipeline/process/processSam2MoleculeTable-PCT48_JAH.pl
cassiopeia/TreeSolver/Cassiopeia_Tree.py
cassiopeia/TreeSolver/Node.py
cassiopeia/TreeSolver/__init__.py
cassiopeia/TreeSolver/binarize_multistate_charmat.py
cassiopeia/TreeSolver/compute_meta_purity.py
cassiopeia/TreeSolver/data_pipeline.py
cassiopeia/TreeSolver/post_process_tree.py
cassiopeia/TreeSolver/reconstruct_sim_tree.py
cassiopeia/TreeSolver/reconstruct_tree.py
cassiopeia/TreeSolver/sample_workflow_ivlt_simulation.py
cassiopeia/TreeSolver/sample_workflow_real_data.py
cassiopeia/TreeSolver/sample_workflow_simulated_data.py
cassiopeia/TreeSolver/score_triplets.py
cassiopeia/TreeSolver/simulate_tree.py
cassiopeia/TreeSolver/utilities.py
cassiopeia/TreeSolver/lineage_solver/ILP_solver.py
cassiopeia/TreeSolver/lineage_solver/__init__.py
cassiopeia/TreeSolver/lineage_solver/greedy_solver.py
cassiopeia/TreeSolver/lineage_solver/lineage_solver.py
cassiopeia/TreeSolver/lineage_solver/solution_evaluation_metrics.py
cassiopeia/TreeSolver/lineage_solver/solver_utils.c
cassiopeia/TreeSolver/lineage_solver/solver_utils.pyx
cassiopeia/TreeSolver/simulation_tools/__init__.py
cassiopeia/TreeSolver/simulation_tools/dataset_generation.c
cassiopeia/TreeSolver/simulation_tools/dataset_generation.pyx
cassiopeia/TreeSolver/simulation_tools/simulation_utils.py
cassiopeia/TreeSolver/simulation_tools/validation.py
cassiopeia_lineage.egg-info/PKG-INFO
cassiopeia_lineage.egg-info/SOURCES.txt
cassiopeia_lineage.egg-info/dependency_links.txt
cassiopeia_lineage.egg-info/entry_points.txt
cassiopeia_lineage.egg-info/not-zip-safe
cassiopeia_lineage.egg-info/requires.txt
cassiopeia_lineage.egg-info/top_level.txt
test/test_error_corrections.py
test/test_reconstruction.py