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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified November 22, 2023
Description: Filters sequences by exact sequence matches.
This can also handle inexact matches but is extremely slow in that mode.
Usage: filterbysequence.sh in=<file> out=<file> ref=<file> include=<t/f>
I/O Parameters:
in= Primary input. 'in2' will specify a second file.
out= Primary out. 'out2' will specify a second file.
ref= A reference file or comma-delimited list of files.
literal= A literal sequence or comma-delimited list of sequences.
ow=t (overwrite) Overwrites files that already exist.
Processing Parameters:
include=f Set to 'true' to include the filtered sequences rather
than excluding them.
rcomp=t Match reverse complements as well.
case=f (casesensitive) Require matching case.
storebases=t (sb) Store ref bases. Requires more memory. If false,
case-sensitive matching cannot be done, and the matching
will be probabilistic based on 128-bit hashcodes.
threads=auto (t) Specify the number of worker threads.
subs=0 Maximum number of substitutions allowed.
mf=0.0 (mismatchfraction) Maximum fraction of bases that can
mismatch. The actual number allowed is the max of subs
and mf*min(query.length, ref.length).
lengthdif=0 Maximum allowed length difference between query and ref.
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="-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 filterbysequence() {
local CMD="java $EA $EOOM $z -cp $CP jgi.FilterBySequence $@"
echo $CMD >&2
eval $CMD
}
filterbysequence "$@"
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