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While manually breaking up lines which were too long, I encountered the same chunk of code copied and pasted many times over and over again in various scripts in scripts/ and sandbox/. We definitely want to place this in a common module for maintainability and reusability reasons.
The text was updated successfully, but these errors were encountered:
The threshold for what collision rate is too high varies in different parts of the code.
-Would you like to keep the thresholds as written, even though they are not consistent?
-Would you like to add this check to the places where collision rate is calculated but not checked?
For now, I will pass the existing thresholds as an argument to the check function, and will use .2 as a default threshold where none is listed.
Here are the places the duplicate logic is found (or should be found?), and their thresholds:
Collect variants -- .2 (with a comment saying don't change)
Collect Reads -- .2 (with a comment saying don't change)
Saturate by med. -- .8 (cites Zhang et al)
do partition -- .15 (with a comment saying the actual max is .18, don't change)
filter abund. single-- no check
load graph -- .15 (with a comment saying the actual max is .18, don't change)
load into c. -- .2
norm by med. -- .8 (cites zhang et al)
trim low abund. -- .8 (cites zhang et al)
Also!
Some places had the opportunity to force listed and others didn't. Is there a pattern to where where you'd like to allow for a force? Right now, I'm fixing as if you want to allow for a force at any time.
While manually breaking up lines which were too long, I encountered the same chunk of code copied and pasted many times over and over again in various scripts in scripts/ and sandbox/. We definitely want to place this in a common module for maintainability and reusability reasons.
The text was updated successfully, but these errors were encountered: