BrendelGroup/AEGeAn — pull request #12 by standage (2014-01-25 21:43:06+00:00)
Title: Added check for top-level features

Based on a suggestion from Jimmy, I've added a check for each feature type to see whether it includes top-level features. Here's the new report.

```
===== Types =====
CDS (includes top-level features)
exon
gene (includes top-level features)
mRNA (includes top-level features)
match (includes top-level features)
ncRNA
primary_transcript
rRNA (includes top-level features)
region (includes top-level features)
tRNA (includes top-level features)
transcript

===== Relationships (child --> parent) =====
CDS --> gene
CDS --> mRNA
exon --> gene
exon --> mRNA
exon --> ncRNA
exon --> primary_transcript
exon --> rRNA
exon --> tRNA
exon --> transcript
mRNA --> gene
ncRNA --> gene
primary_transcript --> gene
tRNA --> gene
transcript --> gene
```

This doesn't mean that every CDS is a top-level feature, but that there is at least one CDS that is a top-level feature (i.e. it has no parents). This will help us track down additional issues.