Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #154. This PR updates code to retain autopvs1 criterion column in final output, and replaces unadjusted evidence columns with autopvs1 adjusted columns

What was your approach?

Evidence column values from intervar adjusted data frame (combined_tab_with_vcf_intervar) were prioritized over those from unadjusted data frame (clinvar_anno_intervar_vcf_df)
criterion was added to output_colnames.tsv

What GitHub issue does your pull request address?

154

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

Which areas should receive a particularly close look?

Please run updated code on custom and pbta test files, and check that criterion_autopvs1 column is retained in final output. Additionally, you can test that adjusted evidence columns are included by checking variants with criterion == "na" and "intervar_adjusted == "Yes"; these should all have PVS1_autogvp == 0.

bash run_autogvp.sh --workflow="cavatica" \
--vcf=input/test_pbta.single.vqsr.filtered.vep_105.vcf \
--filter_criteria='INFO/AF>=0.2 INFO/DP>=15 (gnomad_3_1_1_AF_non_cancer<0.01|gnomad_3_1_1_AF_non_cancer=".")' \
--intervar=input/test_pbta.hg38_multianno.txt.intervar \
--multianno=input/test_pbta.hg38_multianno.txt \
--autopvs1=input/test_pbta.autopvs1.tsv \
--outdir=../results \
--out="test_pbta"

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?

Documentation Checklist

[X] The function has examples to showcase the usage

diskin-lab-chop / AutoGVP

Save criterion and adjusted evidence cols in final output #155