Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #130. This PR modifies the address_conflicting_interp() to only loop through variants with Stars == "1NR".

What was your approach?

Added a line in function code to filter clinvar_anno_vcf_df for only variants with Stars == "1NR". This will reduce time taken to run the function since not all variants will be looped through.

What GitHub issue does your pull request address?

130

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

Which areas should receive a particularly close look?

Please review new code logic and run test_pbta and custom test files

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

update address_conflicting_interp() #135