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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified July 6, 2015
Description: Filters lines by exact match or substring.
Usage: filterlines.sh in=<file> out=<file> names=<file> include=<t/f>
Parameters:
include=f Set to 'true' to include the filtered names rather than excluding them.
prefix=f Allow matching of only the line's prefix (all characters up to first whitespace).
substring=f Allow one name to be a substring of the other, rather than a full match.
f: No substring matching.
t: Bidirectional substring matching.
line: Allow input lines to be substrings of names in list.
name: Allow names in list to be substrings of input lines.
case=t (casesensitive) Match case also.
ow=t (overwrite) Overwrites files that already exist.
app=f (append) Append to files that already exist.
zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
names= A list of strings or files, comma-delimited. Files must have one name per line.
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.
To read from stdin, set 'in=stdin'. The format should be specified with an extension, like 'in=stdin.fq.gz'
To write to stdout, set 'out=stdout'. The format should be specified with an extension, like 'out=stdout.fasta'
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="-Xmx800m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 800m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
function filterlines() {
local CMD="java $EA $EOOM $z -cp $CP driver.FilterLines $@"
echo $CMD >&2
eval $CMD
}
filterlines "$@"
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