extend_length — extend_length • minSNPs

extend_length extend the search sequence such that there will always be (prev) bases before the SNPs and (after) bases after the SNPs.

extend_length(
  overlaps,
  position_reference,
  genome_position,
  prev,
  after,
  ori_string_start,
  ori_string_end,
  ori_snp_pos,
  genome_max
)

Arguments

overlaps: Overlappings
position_reference: the mapping of position in SNP matrix to reference genome
genome_position: the position of the SNP in the reference genome
prev: number of bases before the SNP included in the search string
after: number of bases after the SNP included in the search string
ori_string_start: original starting point of search string
ori_string_end: original ending point of the search string
ori_snp_pos: original SNP position in search string
genome_max: length of the reference genome

Value

a list containing the new `string_start`, `string_end`, `snp_pos`, `snps_in_string`.