-
Notifications
You must be signed in to change notification settings - Fork 5
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
getEndQuery() and getEndRef() returning 0 #2
Comments
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. |
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.
The text was updated successfully, but these errors were encountered: