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No emmsion matrix and transition matrix generated with Spectacle_python.py #3

@BBJamge

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@BBJamge

I have used Spectacle to analyze ChIP seq data in plants. The Java version works fine.But with increasing sample size, it takes longer to run.

And When I use Spectacle python script, there is no generation of emission matrix and transition matrix and not even the emission matrix heatmap png.

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