Kristoffer

Some comments on why I dit it in two separate functions. (also see comments under the function header in the code, lines 535-538) The reference only need seeds created in...

great, I will test this as soon as i have time!

Without commenting at a detailed level. I do think that MAPQ is different if there is extra confidence for the mated read being aligned consistently nearby. This is how i...

Nevermind previous answer (was before coffee :). While my comment still holds, your particular set of observations indeed look suspicious - PE having lower confidence than SE. MAPQ is indeed...

Not at a computer so excuse my brevity and guessing. First, our formula is from minimap2 I believe (see paper) if my memory is correct. If not, it’s from BWA....

I think we can do better because our seeding is different to minimap2 and we should probably should take advantage or at least customize for that. If any mapper is...

@PaulPyl , I am also having problems installing on mac as I reported in https://github.com/ksahlin/StrobeAlign/issues/102. I haven't tried to compile strobealign since before summer though, so cannot say whether this...

I wish I had a good solution for this. I think the MAPQ question is more of an open-ended research question. Do the reads seem to have a more logical...

Thanks for the detailed answer! Yes, I think this sounds great and worth spending some time on since it is beneficial for the code base regardless.

I agree with this. Probably an artefact of using SSW local alignment mode. I used ksw2 before, but found its extension mode to occasionally yield some strange alignments over indels,...