MANIFEST.in
README.md
setup.cfg
setup.py
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remixt/bamreader.pyx
remixt/bpmodel.cpp
remixt/bpmodel.pyx
remixt/cn_model.py
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remixt/defaults.py
remixt/likelihood.py
remixt/ref_data.py
remixt/segalg.py
remixt/seqdataio.py
remixt/utils.py
remixt/visualize.py
remixt/workflow.py
remixt.egg-info/PKG-INFO
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remixt/analysis/__init__.py
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remixt/analysis/experiment.py
remixt/analysis/gcbias.py
remixt/analysis/haplotype.py
remixt/analysis/pipeline.py
remixt/analysis/readcount.py
remixt/analysis/readdepth.py
remixt/analysis/segment.py
remixt/analysis/stats.py
remixt/analysis/temp.py
remixt/mappability/__init__.py
remixt/mappability/tasks.py
remixt/mappability/bwa/__init__.py
remixt/mappability/bwa/workflow.py
remixt/simulations/__init__.py
remixt/simulations/balanced.py
remixt/simulations/experiment.py
remixt/simulations/haplotype.py
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remixt/tests/test_likelihood.py
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remixt/tests/test_segalg.py
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remixt/tests/unopt/model.py
remixt/ui/__init__.py
remixt/ui/create_ref_data.py
remixt/ui/main.py
remixt/ui/mappability_bwa.py
remixt/ui/plot_results.py
remixt/ui/run.py
remixt/ui/visualize_solutions.py
remixt/ui/write_results.py
remixt/wrappers/__init__.py
remixt/wrappers/cmdline.py
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remixt/wrappers/wrapclonehd.py
remixt/wrappers/wrapremixt.py
remixt/wrappers/wraptheta.py
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src/BamAlleleReader.cpp
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src/test.cpp
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