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jit-able bootstrapping of reads #1

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jwschroeder3
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I actually made quite a few changes, which I hope won't mess things up too much.

You'll need to install numba, pandas, and dfply for the code to run.

Note the arguments:

  • I added a required argument, sample_name_luts, which accepts file names with your sample information from the UofM sequencing core. The script creates a lookup table to associate sample_ids with sample descriptions as you gave them to UofM.

  • I changed "ext" to "ChIP" in some arguments.

  • I added the "numba" argument. You must include this argument to use the jitted bootstrapping function. If you don't include --numba at runtime, you'll just use the original sampling function.

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