Armin Töpfer

fwiw, the patch fixes one problem, now it crashes somewhere else in a later stage of the algo. This is going to take a while to get the next core...

The other issue was an out of bound problem in another function that stopped being a problem after I toggled homopolymer compression off.

Ok, good to know. I went with my out of bounds check. Do you think this will cause any problem?

Is the source code available to study?

Feel free to issue a PR. Nobody is working actively on the code base.

Unless you fix it yourself and provide a patch, this issue is not helpful. Even if someone would want to fix it, there is no data to reproduce your problem.

It's likely UB. Another phenotype is aborting with ``` [WFA::Backtrace] Wrong type trace.2 ```

Another UB hit ``` SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior ../subprojects/wfa/wavefront/wavefront_extend.c:116:38 in ../subprojects/wfa/system/mm_allocator.c:400:66: runtime error: addition of unsigned offset to 0x632000000800 overflowed to 0x6320000007f8 ``` @ekg do you have a code snippet to...

Okay, I added it https://github.com/armintoepfer/aligner-testbed/blob/main/src/main.cpp#L168-L215 Anything obviously broken during my copy/paste?

First of all, great to hear that you could run it. I'm using a standard x86 i7 in my iMac with the latest apple clang and gcc11. The issue is...