Closed justaddcoffee closed 4 years ago
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
I found the bug (finally, it really took two weeks to overcome this stupidity...)
+1
For example, this run using the yaml command:![Screen Shot 2019-11-06 at 3 43 33 PM](https://user-images.githubusercontent.com/150311/68348229-3d3def00-00ae-11ea-8b6f-9bc35110b908.png)
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: