Correct blue = rgb[2], was incorrectly set to rgb[3]
Do 2 passes through features in GFFParser (really 3 if you count combining). Implement having all CDSs be treated as a single coding sequence if the ids are different, different coding sequence if any exist with the same ID

GFFCombiner: Turn subFeatures into a queue, so we can remove elements as soon as they are processed easily. Properly remove elements from transcriptCache during iteration through iterator.remove as well
Include exons with no corresponding CDS
Add canonical eden gene from SO unit test
Many more asserts for testEDENSample

In GFFFeatureSource, set exons to be UTR unless there is a CDS feature associated with them
Remove getReadingShift, change to getReadingFrame (redundant)
Add more GFF3 unit tests

Add test for GFF file with no "exon" features (just CDS).
Add file with a tRNA and a (presumably) non-coding exon, check that it is marked noncoding
Add whole-genome summary data for CufflinksDataSource
Merge pull request #36 from broadinstitute/GFF_reader

Gff reader
Remove Alignment caching

Only store one AlignmentInterval per reference frame, using frame name as key. Use Guava MapMaker to create a map with softValues so we don't have any memory leaks.

See IGV-1900, IGV-1881