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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified May 23, 2016
Description: Replaces read names with names from another file.
The other file can either be sequences or simply names, with
one name per line (and no > or @ symbols). If you use one name
per line, please give the file a .header extension.
Usage: replaceheaders.sh in=<file> hin=<headers file> out=<out file>
Parameters:
in= Input sequences. Use in2 for a second paired file.
in= Header input sequences. Use hin2 for a second paired file.
out= Output sequences. Use out2 for a second paired file.
ow=f (overwrite) Overwrites files that already exist.
zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
int=f (interleaved) Determines whether INPUT file is considered interleaved.
fastawrap=70 Length of lines in fasta output.
qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
Renaming modes (if not default):
addprefix=f Rename the read by prepending the new name to the existing name.
Sampling parameters:
reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
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="-Xmx1g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
function reheader() {
local CMD="java $EA $EOOM $z -cp $CP jgi.ReplaceHeaders $@"
echo $CMD >&2
eval $CMD
}
reheader "$@"
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