Ignore inconsistent soft-clips #90
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
brentp
reviewed
Mar 12, 2021
| var b = cl.bounds(max_clip_dist) | ||
| check b.left == 223 | ||
| check b.right == 224 | ||
| check b.left_most == 100 |
There was a problem hiding this comment.
should it drop (or flag) the read(s) that don't fit with the event?
There was a problem hiding this comment.
Yes, that would be better. Because then we could update the center mass and the start/end of the event accordingly. Ideas on how to code that?
There was a problem hiding this comment.
@brentp what are you thinking about this? Do you think it's worth changing the implementation to completely drop those reads rather than just excluding them from the left/right bounds calculation?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
When determining the bounds for a locus, ignore soft-clips that are inconsistent with the center mass.
Ignore left soft-clips that are too far to the right, and right soft-clips that are too far to the left of the center mass.
"Too far" is half the median fragment size.
Possible addition: re-calculate the center mass and far left and right bounds after removing those soft clips?