LeftAlignAndTrimVariants does not handle ##INFO=<Number=R>

tommycarstensentommycarstensen United KingdomMember ✭✭✭

I have attached two VCF files generated with samtools (pass.vcf and fail.vcf). One of them (fail.vcf) contains this line:

##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">

When I run LeftAlignAndTrimVariants3.2 on the v4.2 VCF file containing the INFO line above, then I get this error:

##### ERROR MESSAGE: For input string: "R"

The line is perfectly valid according to the VCF4.2 (and 4.3) specifications:

"The Number entry is an Integer that describes the number of values that can be included with the INFO field." "If the field has one value for each possible allele (including the reference), then this value should be ‘R’."

It's an easy issue to handle, but it would be great, if you could eventually fix this low priority bug. Thanks!

I haven't attached the two small vcf files. "Uploaded file type is not allowed." But zip files are. Files attached.

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