Add AD columns to output

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #179. Added columns AD_ref and AD_alt to full AutoGVP output

What was your approach?

Split VCF FORMAT/AD by , to generate unique columns for ref and alt counts

What GitHub issue does your pull request address?

179

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

Which areas should receive a particularly close look?

Please run on cavatica test files and ensure AD_ref and AD_alt are present in full output.

bash run_autogvp.sh --workflow="cavatica" \
--vcf=input/test_pbta.single.vqsr.filtered.vep_105.vcf \
--filter_criteria='FORMAT/DP>=10 (FORMAT/AD[0:1-])/(FORMAT/DP)>=0.2 (gnomad_3_1_1_AF_non_cancer<0.001|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"

Is there anything that you want to discuss further?

No

Documentation Checklist

• [X] The function has examples to showcase the usage