replace %3D with = in HGVSp

[rjcorb]

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #164. This PR replaces %3D with = in synonymous variant HGVSp values.

What was your approach?

str_replace()

What GitHub issue does your pull request address?

164

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

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

Please run on test data set, and confirm synonymous variant HGVSp value have = and not %3D

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"

Documentation Checklist

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