bowtieIndexToChromSizes <- function(prefix, outname="genome.chrom.sizes"){
cmdString <- paste( "bowtie-inspect -s", prefix, " | grep \"^Sequence\" | awk '{ncol=NF; print $2,$NF}' OFS='\t' | sort -k1,1 > ",outname)
res <- cmdRun(cmdString)
return(outname)
}
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