holmeso commented 2 years ago

Description

The PositionChrPositionMap class was hard-coded to use the GRCh37 reference genome. This has been changed so that any reference index file can be used. A check to see if the generated map contains any overlapping regions has been added.

re #307

Type of change

[X] Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

Additional unit tests have been added. Existing unit tests have been modified. All tests pass.

Are WDL Updates Required?

No

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] 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

ChristinaXu2017 commented 2 years ago

looks good, well tested. There are many old codes commented out, should they be deleted?