extend_length {minSNPs}

extend_length

Description

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

Usage

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'.