Orient #49
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Orient #49
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Looks good. Have the bootstraps been tested? |
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I have tested them and they run. Perhaps someone else should do it just in case. Note that the bias learned in the EM step is passed on to the bootstraps and they don't try to learn it any further. |
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Will merge for now and test on Monday. I don't see anything that looks like it would break the bootstraps. |
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This includes minor changes to the index that allow us to do sequence specific bias.