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UIUCSinhaLab / GEMSTAT

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
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IND Gemstat is sensitive to the order of TFs, (and who knows what else?) #9

Open bryan-lunt opened 9 years ago

bryan-lunt commented 9 years ago

In ExprFunc::predictExpr(...) (ExprPredictor.cpp) we see at least one place where the code assumes that 'cic' will be factor number 2 (0-index, so the third in the factor_expression file.)

This silently and secretly requires the user to have their transcription factors in identical order to what was used in the paper.

bryan-lunt commented 9 years ago

Someone needs to make the main function of the IND gemstat check that CIC is TF number 2, and exit with an appropriate warning if not. Deeper fixes can come later.

bryan-lunt commented 6 years ago

Maybe instead of coding this into a long abandoned branch, we should just add a readme for that branch. It will only get used from now on if someone is checking/reproducing historical results anyway.