extend_length: 'extend_length'

In ludwigHoon/minSNPs: Resolution-Optimised SNPs Searcher

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'.

ludwigHoon/minSNPs documentation built on March 25, 2024, 11:54 a.m.