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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified January 21, 2015
Description: Counts GC content of reads or scaffolds.
Usage: countgc in=<input> out=<output> format=<format>
Input may be stdin or a fasta or fastq file, compressed or uncompressed.
Output (which is optional) is tab-delimited.
format=1: name length A C G T N
format=2: name GC
format=4: name length GC
Note that in format 1, A+C+G+T=1 even when N is nonzero.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}
#This block allows symlinked shellscripts to correctly set classpath.
pushd . > /dev/null
DIR="${BASH_SOURCE[0]}"
while [ -h "$DIR" ]; do
cd "$(dirname "$DIR")"
DIR="$(readlink "$(basename "$DIR")")"
done
cd "$(dirname "$DIR")"
DIR="$(pwd)/"
popd > /dev/null
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
CP="$DIR""current/"
z="-Xmx120m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
countgc() {
local CMD="java $EA $EOOM $z -cp $CP jgi.CountGC $@"
echo $CMD >&2
eval $CMD
}
countgc "$@"
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