Automatically add result of check for CLE validation of each variant

[malachig]

Currently the script generate_reviews_files.py add as a column for "Variant Called by CLE Pipeline" which reviewers must manually check.

neoag_vaccine_scripts/scripts/generate_reviews_files.py

Line 112 in f51ec53

reviewed_candidates["Variant Called by CLE Pipeline"] = " "

This is manual, slow, and potentially error prone and there is really no need for this to be manual.

We should update this script to take an extra input that already has the answer to this question and simply populate the values of this column: True/False. In each run of the immuno pipeline there is a file variants.final.annotated.tsv where the 6th column called VALIDATED contains the result of checking whether each variant called by the immuno.wdl pipeline was also found in the CLE variants ("known variants") file. We can just match up the variants by coordinates and base changes and if there is a match include the value from the VALIDATED in the Variant Called by CLE Pipeline column of the output file produced by generate_reviews_files.py.

[malachig]

To match up variants between the two files compare the first four columns of variants.final.annotated.tsv

CHROM	POS	REF	ALT
chr1	197057393	C	T
chr1	210797717	A	T
chr1	211372430	G	A

To the first column of the neoantigen candidates file (ITB Reviewed Candidates excel file):

ID
chr1-197057392-197057393-C-T
chr1-210797716-210797717-A-T
chr1-211372429-211372430-G-A