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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified August 9, 2018
Description: Generates statistics about flowcell positions.
Seems entirely superceded by filterbytile now; to be removed after 39.12.
Usage: plotflowcell.sh in=<input> out=<output>
Input parameters:
in=<file> Primary input file.
in2=<file> Second input file for paired reads in two files.
indump=<file> Specify an already-made dump file to use instead of
analyzing the input reads.
reads=-1 Process this number of reads, then quit (-1 means all).
interleaved=auto Set true/false to override autodetection of the
input file as paired interleaved.
Output parameters:
out=<file> Output file for filtered reads.
dump=<file> Write a summary of quality information by coordinates.
Tile parameters:
xsize=500 Initial width of micro-tiles.
ysize=500 Initial height of micro-tiles.
size= Allows setting xsize and ysize tot he same value.
target=800 Iteratively increase the size of micro-tiles until they
contain an average of at least this number of reads.
Other parameters:
trimq=-1 If set to a positive number, trim reads to that quality
level instead of filtering them.
qtrim=r If trimq is positive, to quality trimming on this end
of the reads. Values are r, l, and rl for right,
left, and both ends.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 GB of RAM; -Xmx200m will specify
200 MB. 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="-Xmx8g"
z2="-Xms8g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 3200m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
plotflowcell() {
local CMD="java $EA $EOOM $z $z2 -cp $CP hiseq.PlotFlowCell $@"
echo $CMD >&2
eval $CMD
}
plotflowcell "$@"
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