Check that the sequence context information is consistent with the value of the column REF.
Check that the sequence context information is consistent with the value of the column REF.
CheckSeqContextInVCF(vcf, column.to.use)
vcf |
In-memory VCF as a data.frame; must be an SBS or DBS VCF. |
column.to.use |
The column name as a string of the column in the VCF with the context information. |
Throws error with location information if the value of REF is inconsistent with the value of seq.21bases. Assumes the first base of the reference allele is at position (size(<context string>)-1)/2, and generates error if this is not an integer. Indices are 1-based.
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