Creates and names a chromR object from a name, a chromosome (an ape::DNAbin object), variant data (a vcfR object) and annotation data (gff-like).
The function create.chromR is a wrapper which calls functions to populate the slots of the chromR object.
The function vcf2chromR is called by create.chromR and transfers the data from the slots of a vcfR object to the slots of a chromR object.
It also tries to extract the 'DP' and 'MQ' fileds (when present) from the fix slot's INFO column.
It is not anticipated that a user would need to use this function directly, but its placed here in case they do.
The function seq2chromR is currently defined as a generic function.
This may change in the future.
This function takes an object of class DNAbin and assigns it to the 'seq' slot of a chromR object.
The function ann2chromR is called by create.chromR and transfers the information from a gff-like object to the 'ann' slot of a chromR object.
It is not anticipated that a user would need to use this function directly, but its placed here in case they do.