The PR adds more information to GenotypeLrWithExplanation to allow better explanation of genotype LRs downstream.
The new enum GenotypeLrMatchType is conceptually similar to LrMatchType and describes the route of genotype LR calculation. Based on the enum value, the downstream code can determine how many causal variants need to be searched for and presented in the report.
@pnrobinson while working with the code, I also wanted to address #616 . Basically, we will NEVER include the variants with primary ClinVar interpretation from one of the following into consideration, when calculating the number of pathogenic alleles or pathogenicity bin score for a gene:
BENIGN
LIKELY_BENIGN
BENIGN_OR_LIKELY_BENIGN
@pnrobinson can you please comment if this is what you wanted in #616, #592 and #586 ?
The PR adds more information to
GenotypeLrWithExplanationto allow better explanation of genotype LRs downstream.The new enum
GenotypeLrMatchTypeis conceptually similar toLrMatchTypeand describes the route of genotype LR calculation. Based on the enum value, the downstream code can determine how many causal variants need to be searched for and presented in the report.@pnrobinson while working with the code, I also wanted to address #616 . Basically, we will NEVER include the variants with primary ClinVar interpretation from one of the following into consideration, when calculating the number of pathogenic alleles or pathogenicity bin score for a gene:
@pnrobinson can you please comment if this is what you wanted in #616, #592 and #586 ?