BrendelGroup / AEGeAn

Integrated toolkit for analysis and evaluation of annotated genomes
http://brendelgroup.github.io/AEGeAn
ISC License
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Add `-m|--minlength` to locuspocus, iLocus parsing #77

Closed standage closed 10 years ago

standage commented 10 years ago

It doesn't make sense to have, for example, a 2bp iLocus. The idea behind this parameter would be to set a lower limit on iLocus length. If in parsing iLoci we find an iLocus that does not meet this length requirement, it should be incorporated into the adjacent iLocus (if it is terminal) or both adjacent iLoci (if it is internal).

standage commented 10 years ago

By the way, the final solution ended up using the delta parameter instead of a new minlength parameter. The idea is that if the normal parsing procedure is about to create a gene-less iLocus whose length is < ∆, then this iLocus will simply be split evenly between flanking gene-containing iLoci.