Do you want to request a feature or report a bug?
Report a bug
What is the current behavior?
For this VCF row (from 1000 Genomes VCF): 'chr6 18128428 . T A . . NS=1;AN=2;AC=2;CGA_XR=dbsnp.52|rs7886;CGA_FI=7172|NM_000367.2|TPMT|UTR3|UNKNOWN-INC GT:PS:FT:GQ:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL:DP:AD:CGA_RDP 1/1:.:PASS:115:891,115:891,115:49,52:-891,-115,0:-52,-49,0:54:54,54:0'
I get this Java error: 'Error parsing VCF data line'
If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar.
Uploaded 'HG00655.b38.rev.vcf.txt'
What is the expected behavior?
Valid VCF files should parse
What is the motivation / use case for changing the behavior?
Would prefer to not have to manipulate VCFs in order to submit them to PharmCAT.
Please tell us about your environment:
PharmCAT Version: 0.6.0
JDK Version: java version "1.8.0_161"
Environment: Windows
Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, eg. stackoverflow, gitter, etc)
Thanks!
HG00655.b38.rev.vcf.txt
markwoon
commented
3 years ago
Do you want to request a feature or report a bug? Report a bug
What is the current behavior? For this VCF row (from 1000 Genomes VCF): 'chr6 18128428 . T A . . NS=1;AN=2;AC=2;CGA_XR=dbsnp.52|rs7886;CGA_FI=7172|NM_000367.2|TPMT|UTR3|UNKNOWN-INC GT:PS:FT:GQ:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL:DP:AD:CGA_RDP 1/1:.:PASS:115:891,115:891,115:49,52:-891,-115,0:-52,-49,0:54:54,54:0'
I get this Java error: 'Error parsing VCF data line'
If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar. Uploaded 'HG00655.b38.rev.vcf.txt'
What is the expected behavior? Valid VCF files should parse
What is the motivation / use case for changing the behavior? Would prefer to not have to manipulate VCFs in order to submit them to PharmCAT.
Please tell us about your environment:
Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, eg. stackoverflow, gitter, etc) Thanks! HG00655.b38.rev.vcf.txt