Closed TDMedina closed 5 years ago
Is this in build_fastqs_from_donors() ?
@MatthieuBeukers pointed out that not in
may still search through the entire list for a match, then simply inverse the true/false result, meaning there is no speed improvement. Need to check this.
Also, I think reads_to_filter
is a set, not a list, so the search isn't linear and speed won't improve either way.
Also, yes:
Is this in build_fastqs_from_donors() ?
When writing the acceptor FastQ reads to the new combined FastQ, the variant context reads are filtered out. But I just noticed that the logic is:
This means that we have to check EVERY read in the filter list every single time to make sure that NONE of them are a match. If we reverse the logic like this:
Then I would guess that the search through the filter list could exit as soon as it finds a match. It would probably slightly improve speed by like 2 nanoseconds.