Genotypes not labeled or explained in output when using YAML command

[justaddcoffee]

For example, this run using the yaml command: java -jar target/LIRICAL.jar yaml -y ./no_genotype_labels_yaml.txt using the Pfeiffer.vcf and this yaml produces an unlabeled bar for a genotype in FGFR2 that LIRICAL thinks is relevant:

Compare with the same analysis using this phenopacket command: java -jar target/LIRICAL.jar phenopacket -p ./genotype_label_phenopacket_example.txt -e data/1909_hg19 using this nearly equivalent phenopacket we produce this output with a labeled bar for the FGFR2 genotype, along with a table row with info about the genotype:

[justaddcoffee]

This is possibly the problem - in yaml mode, we are always calling buildPhenotypeHtmlTemplate or buildPhenotypeTsvTemplate even if there is genotype info.

If this.phenotypeOnly is false these should be buildGenoPhenoHtmlTemplate or buildGenoPhenoTsvTemplate

[pnrobinson]

I found the bug (finally, it really took two weeks to overcome this stupidity...)

[justaddcoffee]

+1