filter_tx_by_intron_chain.py - annotate 'isoform class' for all event types (intronic_spliced, ds_spliced, 3'UTR introns etc.)

[SamBryce-Smith]

Haven't added for all yet whoops

[SamBryce-Smith]

Current progress:

• [x] 3'UTR introns (last intron fully contained within annotated last exon)
• [x] Downsteam alternatively spliced (annotated last exon is fully contained within novel last exon)
• [x] Intronic bleedthrough ('internal bleedthrough')
• [x] 3'UTR extensions (overlaps + 3'end is downstream of annotated last exon)
• [x] first intron alternatively spliced (e.g. STMN2)
• [x] internal intron alt spliced (should pick out reference internal introns - overlap (containment) novel last with internal)
• [x] give "other" for everything else (most likely readthrough txipts/ weird 3'UTR related isoforms)

[SamBryce-Smith]

All ticked off as of b57e16e8c39e8ad1f492d71e0370a7e6ab569e69. May return to this in future if further isoform classes come to mind (e.g. readthrough txipts, more refined annotation of 3'UTR events).