Enable splicing gene transcripts

[eweitz]

This adds a "Splice" control, which removes introns from gene structure diagrams. It enables showing mature mRNA.

Overview

The transcript diagrams introduced in #309 include introns, as standard in genome browsers. These standard transcript diagrams each show a primary transcript, or pre-mRNA, which include introns. The new "Splice" control allows users to show the transcript without introns. This represents mature mRNA. Clicking the checkbox control toggles whether introns are sliced out.

User impact

This allows users to examine the relative size of untranslated regions (UTRs, teal) compared to coding sequence (CDS, yellow) -- without being visually overwhelmed by much larger intronic regions. These spliced, more mature mRNA features also more closely portray the molecules that are reversed transcribed into cDNA, then processed in e.g. bulk or single cell RNA-seq studies.

The spliced view can clarify analysis focused on exons. It could be especially powerful if future Ideogram development supported showing sample-level data from BAM / BAI, ATAC-seq, or small variation (e.g. SNPs / SNVs of clinical significance) beside this new exonic view.

Demo

Splice_gene_transcript__Ideogram_2022-09-12.mov

Compare the APOE mature mRNA shown above upon clicking "Splice" to the mRNA diagram in Figure 1 of Wu and Zhao (2016, PMC4829000):

[coveralls]

Coverage decreased (-0.5%) to 85.938% when pulling d75a517 on splice-transcripts into a7e5ceb on master.