Splice junctions, which are isomorphic to the introns they span, but which support other biologically relevant constructors and accessors.

Create a splice junction from a donor position (the last position in the 5' exon) and the acceptor position (the first position in the 3' exon).

Donor position, i.e., the last position in the 5' exon around a junction.

Acceptor position, i.e., the first position in the 3' exon around a junction.

List of splice junctions from a spliced location, in order.

Representation of a genomic transcript, with a gene and a transcript identifier, along with the genomic location of the processed transcript and an optional coding sequence on that transcript.

Just the location of the 5' UTR on the transcript, or Nothing if there is no cds on the transcript or if the cds location begins at the first nucleotide of the transcript--if a region is returned it will have positive length.

Just the location of the 3' UTR on the transcript, or Nothing if there is no cds on the transcript or if the cds location ends at the last nucleotide of the transcript--if a region is returned it will have positive length.

Genomic location of CDS within the transcript

Just the input contigs sorted in stranded order, when all lie on the same strand, or Nothing if they are not all on the same strand.