Fig. 3.

SegmentChains automate many common tasks. a. SegmentChain and Transcript objects automatically convert coordinates between genomic and transcript-relative spaces. b. SegmentChains and Transcripts can therefore convert read alignments or quantitative data aligned to the genome to arrays of values at each position in the chain. c. Subsections (green, pink) of chains can be fetched using start and end points relative to the parental chains. SegmentChains automatically generate the corresponding genomic coordinates. d. Regions of a chain can be masked from computations without altering the chain coordinates