Use our final script "filter_phenotypes.sh" in "filter_variants.sh" to output the phenotypes of all filtered samples. If the xlsx flag is set, the output of filter_phenotypes.sh should be in a separate sheet. If the output is TSV (the default), it will be two files with the same basename and ".phenoytpes" appended before the "filter_phenotypes.sh" output. If the output is stdout, the phenotypes should not be printed. In general, there should be an optional flag to request phenotypes. Also, the location of the "filter_phenotypes.sh script and the input-file argument to it should be added as arguments to this script.
TODO:
[x] Add new arguments: Add arguments to specify the location of the "filter_phenotypes.sh" script, the phenotype input file, and a flag to request phenotype output.
[x] Handle new arguments and conditions: Modify the "filter_variants.sh" script to parse and handle these new arguments. Include logic to call "filter_phenotypes.sh" under the appropriate conditions.
[ ] Manage output formats: Handle different output scenarios (XLSX, TSV, STDOUT) as specified.
Use our final script "filter_phenotypes.sh" in "filter_variants.sh" to output the phenotypes of all filtered samples. If the xlsx flag is set, the output of filter_phenotypes.sh should be in a separate sheet. If the output is TSV (the default), it will be two files with the same basename and ".phenoytpes" appended before the "filter_phenotypes.sh" output. If the output is stdout, the phenotypes should not be printed. In general, there should be an optional flag to request phenotypes. Also, the location of the "filter_phenotypes.sh script and the input-file argument to it should be added as arguments to this script.
TODO: