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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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-x flag is silently ignored in YAML mode #461

Closed justaddcoffee closed 4 years ago

justaddcoffee commented 4 years ago

A minor issue, but conflicting commandline args for prefix is ignored in YAML mode.

For example, using the command and YAML below, the -x flag is silently ignored, and this file is output: label_from_yaml.html The -x flag should probably should either override the YAML and produce this file: label_from_command_line.html or emit a warning message saying the -x flag conflicts with the YAML prefix setting.

java -jar target/LIRICAL.jar yaml -y ./example_data/x_flag_issue/x_flag_issue.yml -x label_from_command_line

---
analysis:
  genomeAssembly: hg19
  vcf: /Users/jtr4v/IdeaProjects/LIRICAL/example_data/pfeiffer/Pfeiffer.vcf
  exomiser: /Users/jtr4v/IdeaProjects/LIRICAL/data/1909_hg19
  transcriptdb: ensembl
hpoIds: ['HP:0001875', 'HP:0031508', 'HP:0002970','HP:0100864','HP:0008450','HP:0001156','HP:0100866']
prefix: label_from_yaml
pnrobinson commented 4 years ago

I think we want the yaml mode to not have additional command line options. This will mean refactoring the JCommander code. I am on it.

pnrobinson commented 4 years ago

done