broadinstitute/IGV — pull request #48 by jsilter (2013-05-31 20:07:21+00:00)
Title: Refactor splice junction counting

This shouldn't be pulled without some review.

We count and store splice junctions always, and filter on demand. This is actually only true for minJunctionCoverage and ignoreStrandedness; we still filter based on minFlankingWidth upon loading (needs revisiting).