Hi Marc, thanks for the quick response.
On Tue, Sep 26, 2017 at 06:45:42PM +0200, Marc Rehmsmeier wrote: > Hi Andreas, > > I am not entirely sure what I was doing there and then. That seems to be > version 2.1.2, correct? Yes, that's correct. We always try to package the latest upstream > In version 2.1.1, the array is allocated with ALPHASIZE+1. The <= in the > k-loop is originally not a mistake; the function's sibling, > init_dl_dangle_dg_ar, has the <= in the first loop (the i-loop). These are > the allocations in version 2.1.1: > > double dr_dangle_dg_ar[ALPHASIZE][ALPHASIZE][ALPHASIZE+1]; > double dl_dangle_dg_ar[ALPHASIZE+1][ALPHASIZE][ALPHASIZE]; > > You see that there's a +1 on the corresponding sides. Yes, I see. Would you like to express that the better fix for that issue would be to restore this allocation inside energy.h instead of fixing the loop index? > At some point I introduced an additional letter to the alphabet, the X (a > masking letter; see input.h). I am not sure about the program logic anymore, > whether X can actually be used for lookups in the energy tables (as the N > could). In hybrid_core.c, where the energy functions are used, I check for X > in a few places, so the idea was perhaps to not use X for lookups (in fact, I > do not want to consider any masked sequence at all). Should that be true, > ALPHASIZE being 6 would be wasteful, but it shouldn't harm otherwise. Of > course, you could change the two for-loops (the k-loop in > init_dr_dangle_dg_ar and the i-loop in its sibling) so that they use < > instead of <=, but, while that might fix the array bound bug, it might not > solve an underlying logic problem. In effect you might have a program that > works technically, but produces the wrong result. Unfortunately I can't help > with that. You could try fixing the loops and then do a few runs and compare > the outputs, as a minimal test. So it seems to me that it is safer to leave the loop untouched ... > I hope that helps. Definitely. Thanks again Andreas. -- http://fam-tille.de