Santiago Marco-Sola

@JakeLehle Thanks for the nice words. I'm really glad that the gem3-mapper is useful. Reading this was very rewarding. Thanks.

Hi, Option "--max-reported-matches|-M |'all' (default=5)" should do the trick. By default, it reports a maximum of 4 supplementary. Try first increasing this parameter; let's see it the result meets your...

Ok. Then, let's try to push the mapper a little bit further: > gem-mapper [...] --mapping-mode=sensitive Certainly, this will generate more alt-matches. Don't forget to include '--max-reported-matches 100' or similar....

It's weird. Nonetheless, if you can share index/reference (link to .fa file) and just 1 sequence. I can rerun and try to see what is the problem.

Hi, For the given sequence, they both seem to report the same results. The only difference is that BWA-MEM uses the SA tag and GEM the XA tag. BWA-MEM =>...

Hi, (1) These 2 reads are, in fact, the same read duplicated. Is that what you meant? (2) Both BWA-MEM and GEM report essentially the same (using different tags). BWA...

>Thanks again for your help with this! So is it correct to say that GEM doesn't emit reads with the SA tag or supplementary bit set, but instead encodes the...

I assume you are talking about gap-linear alignment? For the moment, no. The library is slowly incorporating all the features that are planned on the roadmap. If people ask for...

In that case, gap-affine is almost always formulated using {M,X,O,E}, where: M Match Score X Mismatch Penalty O Gap-Opening Penalty E Gap-Extension Penalty So, again, it is symmetric. Sorry. PS....

In the WFA, very likely (for gap-linear). In the GEM, unlikely. At the moment, I don't have enough time to go back to GEM3 and re-implement that part. In the...