Briefly descibe the feature and provide meaningful references
The loading and operations performed on multianno, intervar, and autopvs1 files can be optimized to reduce run time of and memory used by 01-annotate-variants-CAVATICA-input.R and 01-annotate-variants-custom-input.R. Specifically, the following modifications can be made to code associated with these files:
multianno file:
Grouping and arranging commands can be removed, since files come presorted
intervar file:
Creation of var_id can be removed since it is no longer utilized
Grouping and sorting can be removed
autopvs1 file:
vroom() can be used to load file instead of read_tsv()
What input data are required for this feature or analysis?
Modified scripts will be tested on pbta and custom test files
How do you plan to organise the feature or analysis - will it be a multi-function call or add to existing functions?
Only modifying code that already exists in scripts.
Who will complete the feature request (please add a GitHub handle here if relevant)?
Purpose/implementation Section
Briefly descibe the feature and provide meaningful references
The loading and operations performed on multianno, intervar, and autopvs1 files can be optimized to reduce run time of and memory used by
01-annotate-variants-CAVATICA-input.Rand01-annotate-variants-custom-input.R. Specifically, the following modifications can be made to code associated with these files:multianno file:
intervar file:
var_idcan be removed since it is no longer utilizedautopvs1 file:
vroom()can be used to load file instead ofread_tsv()What input data are required for this feature or analysis?
Modified scripts will be tested on pbta and custom test files
How do you plan to organise the feature or analysis - will it be a multi-function call or add to existing functions?
Only modifying code that already exists in scripts.
Who will complete the feature request (please add a GitHub handle here if relevant)?
@rjcorb