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Hi Daniel,
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<div>Your interpretation of the code is correct. keep_preds is a binary setting. There's been some discussion behind-the-scenes about making it more flexible, but that hasn't been implemented yet. We need to fix what it says in the control file. </div>
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<div><span style="font-family: Tahoma; font-size: small; ">Daniel Ence</span></div>
<div><span style="font-family: Tahoma; font-size: small; ">Graduate Student</span></div>
<div><a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">Eccles Institute of Human Genetics</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">University of Utah</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">15 North 2030 East, Room 2100</span><br style="font-family: Tahoma; font-size: small; ">
<span style="font-family: Tahoma; font-size: small; ">Salt Lake City, UT 84112-5330</span></div>
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<div>On May 29, 2014, at 2:37 PM, Daniel Standage <<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>></div>
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<div>Good afternoon!<br>
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I have a quick question about the keep_pred setting in Maker. In older versions of Maker, this was a binary value indicating whether unsupported predictions should be kept. I'm now using Maker 2.31.3, where it's described as a scaled value indicating a "concordance
threshold" for unsupported predictions. As far as I can tell from the code, however, it's still treated in the same way as before.<br>
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Could you briefly describe the motivation for this setting and the intended (although possibly incomplete) change in its functionality in new versions of Maker?<br>
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Thanks!<br clear="all">
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--<br>
Daniel S. Standage<br>
Ph.D. Candidate<br>
Computational Genome Science Laboratory<br>
Indiana University<br>
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