1#!/usr/local/bin/bash 2 3#Running callvariants2.sh is equivalent to running callvariants.sh with the "multi" flag. 4#See callvariants.sh for usage information. 5 6#callvariants2 is intended for multiple sam/bam files, one from each sample, which should have variants called independently; the point is that allele frequencies will be reported for ALL samples at locations where ANY sample has a variant called. 7#callvariants2 is NOT a better version of callvariants, it's the same, just designed for multisample processing. 8#If you have only 1 sample (regardless of how many sam/bam files there are) you should use callvariants.sh without the "multi" flag. 9 10usage(){ 11bash "$DIR"callvariants.sh 12} 13 14#This block allows symlinked shellscripts to correctly set classpath. 15pushd . > /dev/null 16DIR="${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="-Xmx4g" 29z2="-Xms4g" 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 [[ $set == 1 ]]; then 42 return 43 fi 44 freeRam 4000m 84 45 z="-Xmx${RAM}m" 46 z2="-Xms${RAM}m" 47} 48calcXmx "$@" 49 50callvariants2() { 51 local CMD="java $EA $EOOM $z $z2 -cp $CP var2.CallVariants2 $@" 52 echo $CMD >&2 53 eval $CMD 54} 55 56callvariants2 "$@" 57