extend_positions: Add nucleotide positions and extract sequence contexts
In lindberg-m/contextendR: Analyse genomic data with regard to sequence contexts

Add genomic positions to generate a dataset of mutated and non mutated nucleotide positions. Supply known variants either thruogh a data.frame using the 'mut_df' argument, or by supplying the genomic positions and variants throu the three arguments 'chrom', 'pos' and 'alt'. Currently this function will only allow positions where all contextual nucleotides are non-ambiguous.

extend_positions(
  genome,
  N = NULL,
  N_factor = NULL,
  mut_df = NULL,
  chrom = NULL,
  pos = NULL,
  variant = NULL,
  regions.gr = NULL,
  n_max_muts = NULL,
  flank_size = 10,
  num_retries = 10,
  is_pyrbased = F,
  olap = TRUE,
  remove_ambiguous = TRUE
)

`genome`	BSgenome object. The genome which the regions and annotated positions refer to
`N`	Integer. Number of positions to include in final dataset. Can be used instead of 'N_factor'
`N_factor`	Integer. Multiplied with the number of mutations (after subsetting) to reach a target size (instead of specifying directly with 'N')
`mut_df`	data.frame. A data frame containing positions and variant annotations in three columns: 'chrom', 'pos' and 'alt'
`chrom`	Character. A vector of chromosomes. Not necessary if 'mut_df' is supplied
`pos`	Integer. A vector of positions. Not necessary if 'mut_df' is supplied
`variant`	Character. A vector of variants. Not necessary if 'mut_df' is supplied
`regions.gr`	Optional GRanges object. Genomic regions from which to draw random positions
`n_max_muts`	Optional Integer. Filter mutation dataset to only include 'n_max_muts' number of mutations
`flank_size`	Integer. Size of region on each side of mutated and sampled positions to include as contextual regions
`num_retries`	Int
`is_pyrbased`	Bool
`olap`	Bool. Overlap the current mutations with regions?
`remove_ambiguous`	Remove positions where contextual sequences contains ambiguous nucleotides? If so, new positions will be sampled to reach 'N' positions in total