-
Notifications
You must be signed in to change notification settings - Fork 15
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Selecting mapping instance(s) for a read which maps to multiple positions #90
Comments
@martinghunt @iqbal-lab How does that sound? |
Fine with me. So long as we're happy that there are two positions in 5, but uniform random selection is on [1,2,3,4,5], halving the probability of the two positions within site 1 allele 1? |
I'm ok with this, but for option 5, shouldn't it read: Uniform random selection on options within allele 1, followed by Record coverage information for all relevant alleles |
Does that make sense? |
@iqbal-lab OK, updated point 5. |
Cool, just checking i had not misunderstood anything |
@martinghunt This work should be completed with this commit: 47e41d7 This commit also contributed to correctly implementing this issue: 2c776c2 If there are further changes to be made, let's keep them to this issue. |
To discuss after Easter, I think our handling of item 4 is not right. |
@martinghunt @iqbal-lab I'm currently handling this issue: quasimap Assertion `index_end_boundary >= allele_coverage_offset' failed I understand why the error occurs and I've implemented a partial solution. However, that issue has lead me back to this issue. I'm uncertain about how to handle point 6 and point 7 (see first post in this issue: "Quasimapping gives multiple mapping options"). Please help me understand how I should deal with this. |
OK, so suppose we now have A read maps to SEVEN "positions" within the PRG:
A single option is chosen from [1, 7] via uniform random selection. For 1..5 this is identical to above
Completely within an allele is the same as partially overlapping an allele. Record the per-base coverage, and the equivalence-classes/partitions as normal |
@iqbal-lab Thanks! I've updated the first post. |
Sounds good - does this need to be open? |
Quasimapping gives multiple mapping options
A read maps to 7 "positions" within the PRG:
A single option is chosen from [1, 7] via uniform random selection.
Handling Selected Option
The text was updated successfully, but these errors were encountered: