UTF-8 output for synonymous mutations in VCF file

[skurscheid]

Describe the bug
Hi there,

I am observing that the annotated VCF output contains "p.(%3D)" instead of "p.(=)"... I am not sure if this is a local issue, but unfortunately I currently have only access to a single Linux server and insufficient admin privileges to install jannovar anywhere else.

I am using jannovar v0.36 installed via conda.

To Reproduce
Steps to reproduce the behavior:

1. Use the following file or data: https://github.com/skurscheid/bug_reports/blob/0faf92e615b74587100cbe6ef6ea306d591d3509/jannovar/example.vcf
2. Perform the following call:

jannovar annotate-vcf -d ~/Analysis/resources/refs/data/hg19/refseq/refseq_curated_105_hg19.ser --3-letter-amino-acids -i example.vcf -o example.annotated.vcf

3. See error (https://github.com/skurscheid/bug_reports/blob/0faf92e615b74587100cbe6ef6ea306d591d3509/jannovar/example.annotated.vcf)

chr1	98039419	rs56038477	C	T	433	PASS	ANN=T|synonymous_variant|LOW|DPYD|1806|transcript|NM_000110.3|Coding|11/23|c.1236G>A|p.(%3D)|1373/843317|1236/3078|412/1026||;EXON;FC=Synonymous_E412E;GI=DPYD;SNVHPOL=2;SNVSB=-39.6;TI=NM_000110	GT:GQ:GQX:DP:DPF:AD	0/1:466:35:157:13:83,74

Expected behavior

jannovar annotate-pos -d ~/Analysis/resources/refs/data/hg19/refseq/refseq_curated_105_hg19.ser -c 'chr1:98039419C>T'
Options
JannovarAnnotatePosOptions [genomicChanges=[chr1:98039419C>T], toString()=JannovarAnnotationOptions [useThreeLetterAminoAcidCode=false, nt3PrimeShifting=false, showAll=false, databaseFilePath=/home/skurscheid/Analysis/resources/refs/data/hg19/refseq/refseq_curated_105_hg19.ser, toString()=JannovarBaseOptions [reportProgress=true, httpProxy=null, httpsProxy=null, ftpProxy=null, verbosity=1]]]
Deserializing transcripts...
INFO Deserializing JannovarData from /home/skurscheid/Analysis/resources/refs/data/hg19/refseq/refseq_curated_105_hg19.ser
INFO Deserialization took 4.13 sec.
#change effect  hgvs_annotation messages
chr1:98039419C>T        SYNONYMOUS_VARIANT      DPYD:NM_000110.3:c.1236G>A:p.(=)        ..

Additional information

env | grep UTF
LC_ALL=en_US.UTF-8
LANG=en_US.UTF-8
LANGUAGE=en_US.UTF-8

[skurscheid]

I have observed the same behavior on macOS 11.7; installation via conda...