Reverse qualities if needed (merge_methylation_with_metadata() helper)

This function takes a vector of FASTQ qualities and a vector of directions (which must all be either "forward" or "reverse", not case-sensitive) and returns a vector of forward qualities.

Qualities of reads that were forward to begin with are unchanged, while qualities of reads that were reverse are now flipped to give the corresponding forward quality scores.

Called by merge_methylation_with_metadata() to create a forward dataset, alongside reverse_sequence_if_needed(), reverse_locations_if_needed(), and reverse_probabilities_if_needed().

Usage

reverse_quality_if_needed(quality_vector, direction_vector)

Arguments

quality_vector: character vector. The qualities to be reversed. See fastq_quality_scores for an explanation of quality scores.
direction_vector: character vector. Whether each sequence is forward or reverse. Must contain only "forward" and "reverse", but is not case sensitive. Must be the same length as sequence_vector.

Value

character vector. A vector of all forward versions of the input quality vector.

Examples

reverse_quality_if_needed(
    quality_vector = c("#^$&$*", "#^$&$*"),
    direction_vector = c("reverse", "forward")
)
#> [1] "*$&$^#" "#^$&$*"