What is the motivation / use case for changing the behavior?
The number of unique diplotypes from the Matcher JSON files helps determine the fields of the Phenotyper JSON I should process.
Please tell us about your environment:
PharmCAT Version: 2.13.0
JDK Version: openjdk 17.0.6
Environment: [ Windows | macOS | Linux distro | etc ]
Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, e.g. stackoverflow, gitter, etc.)
test_file.zip
bug
For some test samples, Matcher JSON has duplicate CYP2D6 diplotypes under the
-research cyp2d6,combinations
mode.The duplicates can be found under CPIC-CYP2D6-diplotypes. The attached mock VCF will produce a Matcher JSON with two (2)
*1/[*3 + *4 + *122]
This could be reproduced by running
Only one unique diplotype should be reported.
The number of unique diplotypes from the Matcher JSON files helps determine the fields of the Phenotyper JSON I should process.
Please tell us about your environment:
Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, e.g. stackoverflow, gitter, etc.) test_file.zip