allele_diff_indices_parallel2: Calculate SNPs or their count for each germline-input...

In piglet: Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes

Calculate SNPs or their count for each germline-input sequence pair with optional parallel execution.

Description

This function compares germline sequences (germs) and input sequences (inputs) and identifies single nucleotide polymorphisms (SNPs) or their counts, with optional parallel execution. The comparison ignores specified non-mismatch characters (e.g., gaps or ambiguous bases).

Usage

allele_diff_indices_parallel2(
  germs,
  inputs,
  X = 0L,
  parallel = FALSE,
  return_count = FALSE,
  non_mismatch_chars_nullable = NULL
)

Arguments

germs	A vector of strings representing germline sequences.
inputs	A vector of strings representing input sequences.
X	The threshold index from which to return SNP indices or counts (default: 0).
parallel	A boolean flag to enable parallel processing (default: FALSE).
return_count	A boolean flag to return the count of mutations instead of their indices (default: FALSE).
non_mismatch_chars_nullable	A set of characters that are ignored when comparing sequences (default: 'N', '.', '-').

Value

A list of integer vectors (if return_count = FALSE) or a vector of integers (if return_count = TRUE).

Examples

# Example usage
germs <- c("ATCG", "ATCC")
inputs <- c("ATTG", "ATTA")
X <- 0

# Return indices of SNPs
result_indices <- allele_diff_indices_parallel2(germs, inputs, X, 
parallel = TRUE, return_count = FALSE)
print(result_indices)  # list(c(4), c(3, 4))

# Return counts of SNPs
result_counts <- allele_diff_indices_parallel2(germs, inputs, X, 
parallel = FALSE, return_count = TRUE)
print(result_counts)  # c(1, 2)

piglet documentation built on April 12, 2025, 1:27 a.m.