aman 251254f5a9 added the complete work on the 3 hypotheses

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..

aggregate.py

added the complete work on the 3 hypotheses

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call_loops.py

added the complete work on the 3 hypotheses

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perturbation_analysis.py

added the complete work on the 3 hypotheses

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perturbation_viz.py

added the complete work on the 3 hypotheses

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run_genome.sh

added the complete work on the 3 hypotheses

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run.sh

added the complete work on the 3 hypotheses

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