insert_gaps2_vec: Insert gaps into an ungapped sequence based on a gapped...

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

Insert gaps into an ungapped sequence based on a gapped reference sequence.

Description

This function inserts gaps (e.g., . or -) into an ungapped sequence (ungapped) to match the positions of gaps in a reference sequence (gapped). It ensures that the aligned sequence has the same gap structure as the reference.

Usage

insert_gaps2_vec(gapped, ungapped, parallel = FALSE)

Arguments

gapped	A vector of strings representing the reference sequences with gaps.
ungapped	A vector of strings representing the sequences without gaps.
parallel	A boolean flag to enable parallel processing (default: FALSE).

Value

A vector of strings with gaps inserted to match the gapped reference.

Examples

# Example usage
gapped <- c("caggtc..aact", "caggtc---aact")
ungapped <- c("caggtcaact", "caggtcaact")

# Sequential execution
result <- insert_gaps2_vec(gapped, ungapped, parallel = FALSE)
print(result)  # "caggtc..aact", "caggtc---aact"

# Parallel execution
result_parallel <- insert_gaps2_vec(gapped, ungapped, parallel = TRUE)
print(result_parallel)

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