R gist to summarise CIGAR string

cigarfunction.r

matcher <- function(pattern, x) {

  ind = gregexpr(pattern, x)[[1]]
  start = as.numeric(ind)
  end = start + attr(ind, "match.length")- 2
  apply(cbind(start,end), 1, function(y) substr(x, start=y[1], stop=y[2]));
}
doone <- function(c, cigar) {
  pat <- paste("\\d+", c , sep="")
  sum(as.numeric(matcher(pat, cigar)), na.rm=T)
}


## takes a cigar string and parses it, not very fast but...
cigarsums <- function(cigar, chars=c("M","N","D","I","S","H", "P", "X", "=")) {
   sapply (chars, doone, cigar)
}