Marcel Martin

Regarding varying `MAX_LINEAR_SEARCH`: I tried it on CHM13 and set it to various powers of two. There’s no discernible difference in runtime when set to 0, 4 or 256. It...

Documenting another failed attempt at improving speed: In commit 6a5eca7 I tried to make it so that the `partial_queried` vector is not re-created every time the `find_nams` function is run....

Multi-context seeds have been a part of strobealign for a while. I’m closing this PR because it has been split up into smaller PRs that have mostly been merged. The...

Ok, I suggest to focus on the assertion failures in this issue then. Using the most recent sources, here is one way to get such a an assertion failure: ```bash...

Awesome! I’m currently re-running our pipeline with a mason version that includes your patches (and that has assertions enabled). What I spent some time on today is to run this...

Hi, some more info. The backtrace above happens at the very end of the contig when `_alignAndSetCigar` tries to extract a substring of the contig using an end coordinate that...

Thanks for the reply, this is encouraging and I will keep posting the issues I run into. By the way, this is the workflow that I am working on: https://github.com/NBISweden/strobealign-evaluation/blob/main/Snakefile...

> Regarding runtime, you could also compile in `RelWithDebInfo` (or even `Release`) and still get assertions. Adding `-DCMAKE_CXX_FLAGS="-DSEQAN_ENABLE_DEBUG=1"` should be enough for that: Ah, very good! Will try.

Here’s one more, this time on maize (using the above mentioned "sim5" settings). ``` curl https://download.maizegdb.org/Zm-B73-REFERENCE-NAM-5.0/Zm-B73-REFERENCE-NAM-5.0.fa.gz | gunzip > maize.fa mason_variator --sv-indel-rate 0.00002 --snp-rate 0.005 --small-indel-rate 0.001 --max-small-indel-size 100 -ir...

Thank you so much! Sorry for the late reply; I’ve been on vacation until now. I’ll test and report back.