edlibR (version 1.0.3)

getNiceAlignment: Output alignments from align() in NICE format. This outputs the alignment from align() in a visually informative format for human inspection.

Description

Output alignments from align() in NICE format. This outputs the alignment from align() in a visually informative format for human inspection.

Usage

getNiceAlignment(alignResult, query, target, gapSymbol = "-")

Value

Alignment in NICE format, which is an informative visual representation of how the query and target align to each other. e.g., for "telephone" and "elephant", it would look like: telephone |||||.|. -elephant It is represented as an R list with the following fields: - query_aligned (character string) - matched_aligned (character string) ('|' for match, '.' for mismatch, ' ' for insertion/deletion) - target_aligned (character string) Normally you will want to print these three in order above with the function nice_print(), or another method to apply pretty-printing to R lists

Arguments

alignResult

list Output of the method align() Note: align() requires the argument task="path" for 'alignResult' to output a CIGAR for getNiceAlignment() Note: Also, align() requires the argument cigarFormat="extended" in order for getNiceAlignment() to work

query

character string The exact query used for alignResult

target

character string The exact target used for alignResult

gapSymbol

character (default="-") Character used to represent gaps in the alignment between query and target. This must be a single character, i.e. a string of length 1.

Examples

query = "elephant"
target = "telephone"
result = align(query, target, task = "path")
nice_algn = getNiceAlignment(result, query, target)