PaulPyl
PaulPyl
I will keep on working on this next week, I am off tomorrow and Monday. But there is a get_alignment and get_MAPQ function used by align_PE that I want to...
A curious observation here is also, that when I compare my SE result with the test SE result and the test PE result for the same read, the MAPQs are...
I didn't have a lot of time this week to check it more clearly but I was wondering about the current implementation of MAPQ as `// MAPQ = 40(1−s2/s1) ·min{1,|M|/10}...
Thanks, I will have a look over the paper as well. Maybe we need to have a discussion at some point to define what we want to go with. It...
I commit here the changes I wanted to do to align_SE, making it use get_alignment and get_MAPQ internally. The checks fail because the MAPQ values are not identical, but since...
Ok, this PR now compiles again but the checks fail because the MAPQ values are not matching anymore. This relates to #25 but I am unsure how to proceed. We...
I closed this and deleted the branch, I think that issue needs a new run at it. Maybe after addressing the MAPQ score calculation.
You can go ahead and work on align_SE for now, I will let you know if I come back to it.
I don't see any section numbers in the linked paper, both links above point to the same one: [A tandem simulation framework for predicting mapping quality](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1290-3)