Marcel Martin

> will there be some side effects? If AS is the large, how can we ensure the resolution of -A and -B arguments. It should be fine. Since scores are...

@fplaza, You have shown some interest in end-to-end alignment as well. Can you say why you would want it (what is your use case)? We have some code that we...

dnaio already supports reading BAM single-end files (#109). This issue is about improving the support in a couple of ways. What would you need most?

Cutadapt delegates reading and writing sequences to dnaio, so discussing this particular aspect is ok here. That said, do you have a concrete idea of how searching for adapters in...

This just happened again in bioconda/bioconda-recipes#20104 Another example is bioconda/bioconda-recipes#19832

Hi, here comes a late reply because I was on vacation. Let me know how you solved the problem if you have already. Option `-g` allows the adapter to occur...

Thanks for reporting! In short, it appears that the score matrix is not initialized correctly. Let me reply to these comments first: > Would that not imply an alignment like:...

Should now be fixed: ``` $ echo -e '>r\nAATGTCAAA' | cutadapt --quiet -e 1 -g ^AAA - >r GTCAAA ```