Set clinvar clinsig equal to clinvar final call

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #125. The Clinvar_ClinicalSignificance column was reporting calls from the latest clinvar submission, and not the clinvar consensus calls, so there were instances where final_call != Clinvar_ClinicalSignificance.

What was your approach?

For all variants where Reasoning_for_call == "ClinVar", Clinvar_ClinicalSignificance values were set equal to final_call.

What GitHub issue does your pull request address?

125

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Please check new code logic and run custom test files. In abridged output, confirm that, for all variants with autogvp_call_reason == "ClinVar", autogvp_call == clinvar_clinsig.

bash run_autogvp.sh --workflow="custom" \
--vcf=input/test_VEP.vcf \
--clinvar=input/clinvar.vcf.gz \
--intervar=input/test_VEP.hg38_multianno.txt.intervar \
--multianno=input/test_VEP.vcf.hg38_multianno.txt \
--autopvs1=input/test_autopvs1.txt \
--outdir=../results \
--out="test_custom"

Is there anything that you want to discuss further?

I also deleted two print() statements from the custom autogvp R script that were causing all vcf ids to be printed.

[naqvia]

Also can confirm that all 424 calls that have the ClinVar autogvp reason match!