identifySTRRegions takes a fastq-file location or a ShortReadQ-object and identifies the STR regions
based on a directly adjacent flanking regions.
The function allows for mutation in the flanking regions through the numberOfMutation argument.
# S4 method for character
identifySTRRegions(
reads,
flankingRegions,
numberOfMutation = 1,
control = identifySTRRegions.control()
)The returned object is a list of lists. If the reverse complement strings are not included or if the control$combineLists == TRUE,
a list, contains lists of untrimmed and trimmed strings for each row in flankingRegions. If control$combineLists == FALSE, the function returns a list of two such lists,
one for forward strings and one for the reverse complement strings.
path to fastq-file.
containing marker ID/name, the directly adjacent forward and reverse flanking regions, used for identification.
the maximum number of mutations (base-calling errors) allowed during flanking region identification.
an identifySTRRegions.control-object.