query_length is greater than the length of the input sequence

[ekg]

I'm cleaning up the integration of dozeu into vg. (Thanks again @ocxtal !!)

I've run into an issue where it seems that the query_length which dozeu is giving is longer than the actual sequence that has been given for alignment. How could this occur? The result is a big crash, as we try to access sequence that's out of bounds.

[ocxtal]

I noticed now I had mistakenly commented to other place. As a record (and to keep it trackable) I add link and summary of the solution.

• https://github.com/vgteam/vg/pull/1752#issuecomment-402259159
• The problem was caused by inappropriate comparison that chooses longer one for alignments with the same score.
• modifying dz_cmp_max as https://github.com/ocxtal/dozeu/commit/8c905de0aa0fc6c579550b5cfe3374693f266994 prevents it from reporting overrun alignment.

Hajime Suzuki