Allow empty VCF in annotate.sh
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