1#!/usr/local/bin/bash 2 3usage(){ 4echo " 5Description: Generates a histogram of kmer counts for the input reads or assemblies. 6 7Usage: khist.sh in=<input> hist=<histogram output> 8 9Please see bbnorm.sh for more information. 10All the flags are the same, only the parameters (near the bottom of this file) differ. 11" 12} 13 14#This block allows symlinked shellscripts to correctly set classpath. 15pushd . > /dev/null 16DIR="${BASH_SOURCE[0]}" 17while [ -h "$DIR" ]; do 18 cd "$(dirname "$DIR")" 19 DIR="$(readlink "$(basename "$DIR")")" 20done 21cd "$(dirname "$DIR")" 22DIR="$(pwd)/" 23popd > /dev/null 24 25#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" 26CP="$DIR""current/" 27 28z="-Xmx31g" 29z2="-Xms31g" 30set=0 31 32if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then 33 usage 34 exit 35fi 36 37calcXmx () { 38 source "$DIR""/calcmem.sh" 39 setEnvironment 40 parseXmx "$@" 41 if [[ $set == 1 ]]; then 42 return 43 fi 44 freeRam 31000m 84 45 z="-Xmx${RAM}m" 46 z2="-Xms${RAM}m" 47} 48calcXmx "$@" 49 50khist() { 51 local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.KmerNormalize bits=32 ecc=f passes=1 keepall dr=f prefilter hist=stdout minprob=0 minqual=0 mindepth=0 minkmers=1 hashes=3 $@" 52 echo $CMD >&2 53 eval $CMD 54} 55 56khist "$@" 57