biocodz

Can you try `-blast 0` to see the pairwise alignment? (I see your point)

So, it looks like the program stops at a sub-optimal alignment. I'll investigate and get back with the results.

This is not a bug after all. ** It is apparently by design to accelerate the search. The algorithm doesn't necessarily search for exact `local` matches ** The algorithm stops...

That depends on `the best` interpretation. I would define it as an approximate match vs the exact match. The program's goal is to tell the given piece of oligo is...

When a read is aligned against a set of sequences then the alignment with the highest SW **found** would still be `the best`, even if that SW was not `the...

This needs more clarification. I'll keep digging...

Sure. Any suggestions on how exactly to specify this?

Thanks for reporting this. Could you try running using just a single VM instance other than using HPC facilities (to see if the problem persists)? Using Slurm on HPC adds...

can you provide the [execution trace](https://github.com/sortmerna/sortmerna#execution-trace)?

The windows build is broken. Seems it doesn't like the new includes in ssw.c ``` ... 2024-04-04T21:29:00.7066549Z FAILED: src/sortmerna/CMakeFiles/smr_objs.dir/Release/ssw.c.obj 2024-04-04T21:29:00.7990776Z C:\PROGRA~1\MICROS~2\2022\ENTERP~1\VC\Tools\MSVC\1438~1.331\bin\HostX64\x64\cl.exe /nologo -DCMAKE_INTDIR=\"Release\" -ID:\a\sortmerna\sortmerna\include -ID:\a\sortmerna\sortmerna\src\winapi\include -ID:\a\sortmerna\sortmerna\3rdparty\cmph -ID:\a\sortmerna\sortmerna\3rdparty\dirent\include -ID:\a\sortmerna\sortmerna\3rdparty\concurrentqueue -ID:\a\sortmerna\sortmerna\3rdparty\alp -external:ID:\a\sortmerna\sortmerna\build\3rdparty\rocksdb\dist\include...