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Escaped doublequotes in INFO descriptions result in invalid VCF file
Edit 14/03: verified that this also occurs in version 3.0.4
Description of the issue:
When I add a header including a description containing escaped double quotes, sometimes the "escape slash" goes missing, resulting in a invalid VCF file.
Your environment:
- version of htsjdk: 1.24.1 aand 3.0.4
- version of java: OpenJDK 17.0.1
- which OS: Windows and CentOS
Steps to reproduce
VCFHeader newHeader = annotator.annotateHeader(vcfFileReader.getFileHeader());
newHeader(new VCFFormatHeaderLine("TEST", VCFHeaderLineCount.A, VCFHeaderLineType.String,"\"TEST\""));
writer.writeHeader(newHeader);
//... write variants
Expected behaviour
A VCF file is written with an INFO header:
##FORMAT=<ID=TEST,Number=A,Type=String,Description="\"TEST\"">
Actual behaviour
A VCF file is written with an INFO header:
##FORMAT=<ID=TEST,Number=A,Type=String,Description=""TEST\"">
The slash for the first escaped double quote is missing