AnnotationCollection.sortedIterator(annotation, true) returns non-overlapping annotations

[charcuterie]

Tried to get an Iterator which iterates over all fragments in a paired-end bam file that overlap a gene and are fully contained within the gene. The fragments which are returned can have one read of the fragment within the gene, and one outside.

[charcuterie]

Fixed in my branch. Will leave open until changes finalized and rolled into Master

[pamelarussell]

Looks like the method only uses the chr, start, end of the gene, so it also returns reads in the introns. I don't think that's what we want.

[charcuterie]

I'm pretty sure this is fixed, but I'll doublecheck.