bigdatagenomics/adam — pull request #40 by arahuja (2014-01-08 23:11:06+00:00)
Title: Fixing reference position from offset implementation

Two parts here that I wanted to add:

1) Reference position from offset computation was sometimes mapping two different offsets to the same reference position which shouldn't be possible. i.e. if start= 1 and cigar=1S1M we were getting both mapped to 0 as opposed to 0 and 1. Correct me if I'm wrong on my understanding of the cigar.

2) Secondly, end and unclippedEnd are exclusive (pointing to 1 past the last read base) currently, I wanted to know if this was intended? It seemed odd to me that that the final reference position in referencePositions was not the same as end. I think we had started a conversation on reference coordinate system earlier, so curious to know if end is purposely exclusive?

I had changed it and then changed back ...