library(plyr)
library(Rsamtools)
library(GenomicRanges)
library(Biostrings)
library(knitr)

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)
}