hammerlab/immuno — pull request #38 by arahuja (2014-04-09 21:17:55+00:00)
Title: Gets exon start phase information to handle incomplete CDS

- Save phase information from exons
- Compute whether a transcript is off-phase or not
- Change mutation index based on transcript start phase

This handles incomplete CDS due to incomplete upstream 5'. It logs a warning for 5' incomplete but not 3' incomplete (or other definitions of incomplete)