Fails to parse metadata with hypen in the key
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apraga commented
Expected Behavior
Parse a vcf with metadata containg hyphen in the key
##VEP-command-line='vep -i test'
Current Behavior
Fails to parse with ERROR: LoadError: GeneticVariation.VCF.Reader file format error on line 4
Removing the hyphen makes it work.
Possible Solution / Implementation
Steps to Reproduce (for bugs)
Minimal working example.
For this vcf :
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=249250621>
##VEP-command-line='vep -i test'
##FORMAT=<ID=BLT,Number=1,Type=String,Description="High-level location type (het|homref|hetalt|homalt|nocall).">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TRUTH QUERY
The reader
using GeneticVariation
reader = VCF.Reader(open("script/test.vcf"))
fails with
ERROR: LoadError: GeneticVariation.VCF.Reader file format error on line 4
Stacktrace:
[1] error(::String, ::Int64)
@ Base ./error.jl:44
[2] _readheader!(reader::GeneticVariation.VCF.Reader, state::BioCore.Ragel.State{BufferedStreams.BufferedInputStream{IOStream}})
@ GeneticVariation.VCF ~/.julia/packages/BioCore/YBJvb/src/ReaderHelper.jl:106
[3] readheader!(reader::GeneticVariation.VCF.Reader)
@ GeneticVariation.VCF ~/.julia/packages/BioCore/YBJvb/src/ReaderHelper.jl:80
[4] Reader
@ ~/.julia/packages/GeneticVariation/r8DAL/src/vcf/reader.jl:15 [inlined]
[5] GeneticVariation.VCF.Reader(input::IOStream)
@ GeneticVariation.VCF ~/.julia/packages/GeneticVariation/r8DAL/src/vcf/reader.jl:28
[6] top-level scope
@ /Work/Users/XXX/processing/vcf.jl:4
in expression starting at /Work/Users/XXXX/processing/vcf.jl:4
Your Environment
- Package Version used:
- Julia Version used: 1.8.5
- Operating System and version (desktop or mobile): Rocky Linux 8.5
- Link to your project: