Extra annotations to transcriptome-assembly.

1) use the main reference as a scaffold for newly assembled transcripts,
this keeps known gene_ids and transcript_ids and places novel transcripts
of a known gene_id on the known gene_id
2) broadly classify as lincRNA, ncRNA and protein_coding by training
a logistic model to classify non_coding and coding transcripts in
the known reference.
3) remove some Cufflinks specific garbage transcripts such as single exon
novel genes