Marcel Martin

I think you need to install the GNU version of `libtool`, which appears [to be called `glibtool` on macOS](https://stackoverflow.com/questions/54078839/). Maybe `brew install libtool`?

> Trusting you in that there is no substantial speed trade-off for few cores I approve a merge. I’ve done a few more tests to convince myself. On my local...

We don’t support strobealign on Windows at the moment. If it compiled previously, that was a happy accident. If you would like us to support Windows, can you open a...

I’ve now started to run the same optimization as above on the new "Sim5" dataset (the above was done on the "Sim3" dataset, which has less variation). Here are the...

> Oh, is the Before column referring to strobealign with mcs but with parameters from (https://github.com/ksahlin/strobealign/commit/4c10938ac1e88f90f1585eb10c75d33109a2bd64) ? Then I misunderstood. Yes, I essentially re-did the optimization for mcs using SIM5...

I have filled in the [table above](https://github.com/ksahlin/strobealign/issues/423#issuecomment-2117100178). Here is the same table but with numbers relative to d9d5aaf. Readl. | Before | Optimized | maponly SE | maponly PE |...

Hi, the limit is so because the indexing data structure that strobealign uses reserves 24 bits for the contig index. The maximum number of contigs is thus $2^{24}=16777216$. (I think...

I’ve been working on this today. I looked at the set of reads whose alignment becomes incorrect when switching from symmetric to asymmetric randstrobes (using CHM13-500-se). I found that about...

The `-L` is indeed a reward and I have still on my to-do list to document this better. It’s called an *end bonus*. It should work like an end penalty,...

Would you filter out negative AS values? I think you can do the equivalent here: Use `-L 10000` and then filter alignments with AS < 10000. Regular alignments without any...