1#!/usr/local/bin/bash 2 3usage(){ 4echo " 5Written by Brian Bushnell 6Last modified January 21, 2015 7 8Description: Merges coverage stats lines (from pileup) for the same OTU, 9 according to some custom naming scheme. 10 11Usage: mergeOTUs.sh in=<file> out=<file> 12 13Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 14" 15} 16 17#This block allows symlinked shellscripts to correctly set classpath. 18pushd . > /dev/null 19DIR="${BASH_SOURCE[0]}" 20while [ -h "$DIR" ]; do 21 cd "$(dirname "$DIR")" 22 DIR="$(readlink "$(basename "$DIR")")" 23done 24cd "$(dirname "$DIR")" 25DIR="$(pwd)/" 26popd > /dev/null 27 28#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" 29CP="$DIR""current/" 30 31z="-Xmx1g" 32set=0 33 34if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then 35 usage 36 exit 37fi 38 39calcXmx () { 40 source "$DIR""/calcmem.sh" 41 setEnvironment 42 parseXmx "$@" 43} 44calcXmx "$@" 45 46function mergeOTUs() { 47 local CMD="java $EA $EOOM $z -cp $CP driver.MergeCoverageOTU $@" 48 echo $CMD >&2 49 eval $CMD 50} 51 52mergeOTUs "$@" 53