You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
The reason will be displayed to describe this comment to others. Learn more.
I noticed through my own investigations that for the "slack" (set to 10 above) to have the intended effect as implemented above, that is, to join nearby NAMs, it needs to be coupled with if (n.query_end + slack < h.query_start) { and auto c = h.query_start - slack; on lines 114 and 1126 in this commit, respectively. This is to avoid these open NAMs get filtered out before they have a chance to be joined.
I also set int slack = read_length/3; at the start of the function (passing in read length as parameter).
I should also note that I didn't implement any of the previous commits on this branch, I only tested the 'slack' idea.
With my additional changes, I did some local benchmarking on a small test dataset and I cannot observe a clear benefit as of now for any of the read lengths. Accuracy typically an increase or decrease in 0.01 percent points. Although, my tests were coupled with other changes such as asymmetric seeds, no rescue and only benchmarking on chrX+Y.
3d96321There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I noticed through my own investigations that for the "slack" (set to 10 above) to have the intended effect as implemented above, that is, to join nearby NAMs, it needs to be coupled with
if (n.query_end + slack < h.query_start) {andauto c = h.query_start - slack;on lines 114 and 1126 in this commit, respectively. This is to avoid these open NAMs get filtered out before they have a chance to be joined.I also set
int slack = read_length/3;at the start of the function (passing in read length as parameter).I should also note that I didn't implement any of the previous commits on this branch, I only tested the 'slack' idea.
With my additional changes, I did some local benchmarking on a small test dataset and I cannot observe a clear benefit as of now for any of the read lengths. Accuracy typically an increase or decrease in 0.01 percent points. Although, my tests were coupled with other changes such as asymmetric seeds, no rescue and only benchmarking on chrX+Y.