Consider major allele for Homoplasmic vs Heteroplasmic

[Rohan-cod]

Prerequisites

• I am running the latest version
• I checked the documentation and found no answer
• I checked to make sure that this issue has not already been filed

• Package Version: latest
• Operating System: macOS

Expected Behavior

Consider both, ALT allele depth and REF allele depth and use the major allele for Homoplasmic vs Heteroplasmic.

Current Behavior

We consider only ALT allele depth for Homoplasmic vs Heteroplasmic

[Rohan-cod]

Example:

Scenario where reference allele is the minor allele:
Reference allele: A --> 1
Alternative allele: T --> 99

REF allele depth -> 1/100 = 0.01
ALT allele depth-> 99/100 = 0.99

If >0.99 then Homoplasmy; Here it would be Homoplasmy

Scenario where alternative allele is the minor allele:
Reference allele: A --> 99
Alternative allele: T --> 1

REF allele depth -> 99/100 --> 0.99
ALT allele depth-> 1/100 = 0.01

If >0.99 then Homoplasmy; Here it would be Heteroplasmy