getEndQuery() and getEndRef() returning 0

[iagorios]

Hi Jeff,
I'm getting 0 as return when calling getEndQuery() and getEndRef() after NW. It's working when I call SW functions though.
Seems like getLength(), getMatches() and getSimilar() are returning only 0 as well.
Thank you in advance.

[jeffdaily]

getEndQuery() and getEndRef() should return the end locations of the alignment. For SW, parasail follows the example of other alignment packages. For SG and NW alignment, I wasn't aware of what other packages might do. I think for NW I eventually made C parasail just assign the length of the query and target sequences to those attributes because NW is the global end-to-end alignment. For semi-global, I report the actual end of the alignment like I would for SW. Since SG doesn't penalize end gaps, either the end query or end ref will be the length and the remaining sequence will report where the alignment ended. I hope I explained that okay.

BTW, I just updated the java bindings to report the SAM CIGAR if you use the new trace functions, e.g., sw_trace. This is a new feature from the C parasail 2.x release.