The Compare class within qsignature needs to make decisions on whether a snp is hom or het. It uses 3 values to determine this:
hom cutoff (defaults to 0.9)
lower het cutoff (defaults to 0.3)
upper het cutoff (defaults to 0.7)
There are 3 existing options that allow the user to override these defaults, however, the Compare class does not take these into account.
This PR rectifies this oversight, allowing the user to set the cutoffs as they see fit.
A record of the cutoffs used is now added to the xml output so that the viewer can tell what cutoffs were used.
Type of change
Please delete options that are not relevant.
[X] New feature (non-breaking change which adds functionality)
How Has This Been Tested?
Existing unit tests have been updated and new tests added.
Are WDL Updates Required?
No wdl updates are required.
It is anticipated that once this change is in master, an update to the SDFTM wdl workflow will be made to supply cutoff values to qsignature.
Checklist:
[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[X] I have made corresponding changes to the documentation
[X] My changes generate no new warnings
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes
Description
The
Compareclass withinqsignatureneeds to make decisions on whether a snp is hom or het. It uses 3 values to determine this:There are 3 existing options that allow the user to override these defaults, however, the
Compareclass does not take these into account.This PR rectifies this oversight, allowing the user to set the cutoffs as they see fit.
A record of the cutoffs used is now added to the xml output so that the viewer can tell what cutoffs were used.
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Existing unit tests have been updated and new tests added.
Are WDL Updates Required?
No wdl updates are required. It is anticipated that once this change is in master, an update to the
SDFTMwdl workflow will be made to supply cutoff values toqsignature.Checklist: