Move grabbing input FASTQ/BAM files to the datadict module.
Index the transcriptome and align to it with bwa-mem.

This is a bailout strategy for programs needing the transcriptome-aligned
reads right now, but could be used for a super-fast RNA-seq implementation.
Update the data dictionary in place when aligning with STAR.

This lets us put the transcriptome-mapped reads in the datadict
directly, instead of handling it later.
Generate transcriptome-mapped reads on the fly.

Also generates the transcriptome reference file if it does not exist, filtering
out the erroneous transcripts by skipping them if we have already seen them.
This is a relatively cheap operation and lets users use this functionality without
updating the genome files.
Add rsem=True to the RNA-seq integration tests.