Open bjhall opened 6 years ago
If the VCF has "CLNSIG=Likely_pathogenic;", it will incorrectly match the Pathogenic-rule (which has higher priority than the Likely pathogenic-rule, since "Pathogenic" is a substring of "Likely_pathogenic" (case insensitive).
This appears to be the code doing the matching: https://github.com/moonso/extract_vcf/blob/master/extract_vcf/plugin.py#L342
Minimal example files: minimal_rankmodel_string.ini.txt minimal_string.vcf.txt
$ genmod score -i test -c minimal_rankmodel_string.ini.txt -r minimal_string.vcf.txt -o minimal_string.score
Gives me RankResult=5 (for Pathogenic), rather than the expected 2 (for Likely_pathogenic)!
If the VCF has "CLNSIG=Likely_pathogenic;", it will incorrectly match the Pathogenic-rule (which has higher priority than the Likely pathogenic-rule, since "Pathogenic" is a substring of "Likely_pathogenic" (case insensitive).
This appears to be the code doing the matching: https://github.com/moonso/extract_vcf/blob/master/extract_vcf/plugin.py#L342
Minimal example files: minimal_rankmodel_string.ini.txt minimal_string.vcf.txt
$ genmod score -i test -c minimal_rankmodel_string.ini.txt -r minimal_string.vcf.txt -o minimal_string.scoreGives me RankResult=5 (for Pathogenic), rather than the expected 2 (for Likely_pathogenic)!