vmatchPattern2

# From: https://support.bioconductor.org/p/58350/

vmatchPattern2 <- function(pattern, subject,
                              max.mismatch=0, min.mismatch=0,
                              with.indels=FALSE, fixed=TRUE,
                              algorithm="auto")
   {
     if (!is(subject, "XStringSet"))
         subject <- Biostrings:::XStringSet(NULL, subject)
     algo <- Biostrings:::normargAlgorithm(algorithm)
     if (Biostrings:::isCharacterAlgo(algo))
         stop("'subject' must be a single (non-empty) string ",
              "for this algorithm")
     pattern <- Biostrings:::normargPattern(pattern, subject)
     max.mismatch <- Biostrings:::normargMaxMismatch(max.mismatch)
     min.mismatch <- Biostrings:::normargMinMismatch(min.mismatch,
max.mismatch)
     with.indels <- Biostrings:::normargWithIndels(with.indels)
     fixed <- Biostrings:::normargFixed(fixed, subject)
     algo <- Biostrings:::selectAlgo(algo, pattern,
                                     max.mismatch, min.mismatch,
                                     with.indels, fixed)
     C_ans <- .Call2("XStringSet_vmatch_pattern", pattern, subject,
                     max.mismatch, min.mismatch,
                     with.indels, fixed, algo,
                     "MATCHES_AS_RANGES",
                     PACKAGE="Biostrings")
     unlisted_ans <- IRanges(start=unlist(C_ans[[1L]],
use.names=FALSE),
                             width=unlist(C_ans[[2L]],
use.names=FALSE))
     relist(unlisted_ans, C_ans[[1L]])
   }