When doing all-vs-all do not look for anchors of reads with the same read_id. Currently we are doing this for the sake of code simplicity, but this introduces additional overlaps which probably affect accuracy and definitely affect performance by creating additional anchors which take up more space and require time to be processed.
There are two options:
1) Make Matcher not look for anchors with the same read_id
2) If 1) turns out to be too complicated simply skip matching same indices. This would lead to all read pairs from those indices to be skipped, so option 1) is preferred
mimaric
commented
4 years ago
When doing all-vs-all do not look for anchors of reads with the same
read_id. Currently we are doing this for the sake of code simplicity, but this introduces additional overlaps which probably affect accuracy and definitely affect performance by creating additional anchors which take up more space and require time to be processed.There are two options: 1) Make
Matchernot look for anchors with the sameread_id2) If1)turns out to be too complicated simply skip matching same indices. This would lead to all read pairs from those indices to be skipped, so option1)is preferred