Intron genes and ciLoci

[standage]

In an earlier version of AEGeAn, intron genes (gene A completely encompassed by an intron from gene B) were designated as complex iLoci (ciLoci): both the intron gene and the gene containing it were associated with a single ciLocus.

Later, in the context of hiLoci I think, we decided that intron genes could be parsed and handled separately. Currently intron gene cases yield two siLoci, the smaller of which is contained completely within the other.

We're agreed that we don't want to designate such cases as miLoci when merging tightly packed genes. But in terms of classification, does it make more sense to designate the larger gene a ciLocus? Or both genes?

[standage]

For the record:

• The outer gene in intron gene events will be designated as a ciLocus.
• Such genes, as with all ciLoci, will be exempted from merging into miLoci.
• Internal genes will retain siLocus designation but are also exempt from merging.

Will need to confirm that the hiLocus procedure works as expected with the change in designation.