Handle adding of additional hyperlinks to external resources not from standard VEP annotation in the VCF, now will handle decipher, oncoKB, PeCan and cBioPortal.
Changes
New input --additional_columns , list of strings of columns to add
map_chr_to_nc() moved from vcf.py to utils.py (no changes to function)
new class buildHyperlink(), contains all logic for generating hyperlinks (moved and extended from vcf.make_hyperlinks())
Handle adding of additional hyperlinks to external resources not from standard VEP annotation in the VCF, now will handle decipher, oncoKB, PeCan and cBioPortal.
Changes
--additional_columns, list of strings of columns to addmap_chr_to_nc()moved fromvcf.pytoutils.py(no changes to function)buildHyperlink(), contains all logic for generating hyperlinks (moved and extended fromvcf.make_hyperlinks())Test job: https://platform.dnanexus.com/projects/GX1K52Q4KK64pp0x709gj2Qy/monitor/job/GXJF8884KK6F9zKQpp111Fbz
This change is