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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified April 30, 2019
Description: Performs set operations on VCF files:
Union, intersection, and subtraction.
Usage: comparevcf.sh in=<file,file,...> out=<file>
I/O parameters:
in=<file> Input; must be at least 2 files.
out=<file> Output file.
ref=<file> Reference file; optional. Usually not needed.
shist=<file> (scorehist) Output for variant score histogram.
overwrite=f (ow) Set to false to force the program to abort rather than
bgzip=f Use bgzip for gzip compression.
Processing Mode (choose one only):
subtract=t Subtract all other files from the first file.
union=f Make a union of all files.
intersection=f Make an intersection of all files.
Processing Parameters:
addsamples=t Include all samples in the output lines. (TODO)
splitalleles=f Split multi-allelic lines into multiple lines.
splitsubs=f Split multi-base substitutions into SNPs.
canonize=t Trim variations down to a canonical representation.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
specify 200 megs. The max is typically 85% of physical memory.
-eoom This flag will cause the process to exit if an out-of-memory
exception occurs. Requires Java 8u92+.
-da Disable assertions.
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="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 4000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
comparevcf() {
local CMD="java $EA $EOOM $z $z2 -cp $CP var2.CompareVCF $@"
echo $CMD >&2
eval $CMD
}
comparevcf "$@"
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