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Allow empty VCF in annotate.sh

sjurug requested to merge allow-empty-analyses-in-import into dev

Allow empty analyses in import

Closes #8 (closed)
Related: ella#209 (closed)

Allows empty VCFs as input to annotate.sh VEP would otherwise fail for empty VCFs The only requirement is that the VCF has at least one line starting with '#', i.e. that it is a VCF file

Type of change

  • Allow empty VCF

Testing

  • Testing done by running ./annotate.sh --vcf empty.vcf
  • Verified that non-empty VCFs still work by ./annotate.sh --vcf /anno/tests/testdata/brca_sample_composed.vcf

No additional testing

Other

One risk is the use of grep. Used a method that is "guaranteed" when at least one line starting with '#' in VCF

Checklist:

  • I have performed a self-review of my own code
  • My code and commit messages follows the style guidelines in Code Review checklist procedure
  • I have commented my code, particularly in hard-to-understand areas
  • My branch has recently been updated with new changes in dev (and tested) before this merge request
  • I have made corresponding changes to the documentation (state where)
Edited by Morten C. Eike

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