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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified September 11, 2019
Description: Uses paired read insert sizes to estimate the correct
length of scaffold gaps, and resizes incorrectly-sized gaps.
Usage: fixgaps.sh in=mapped.sam ref=scaffolds.fa out=fixed.fa
Standard parameters:
in=<file> Reads mapped to the reference; should be sam or bam.
ref=<file> Reference; may be fasta or fastq.
out=<file> Modified reference; may be fasta or fastq.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
Processing parameters:
gap=10 Consider any consecutive streak of Ns at least this long to
be a scaffold break. Gaps will not be resized to less than
this.
border=0.4 Ignore the outermost (border*readlen) of an insert (read pair)
when incrementing coverage. A higher value is more accurate
but requires more coverage and/or longer inserts. Range: 0-1.
mindepth=10 Minimum spanning read pairs to correct a gap.
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${RAM}m"
}
calcXmx "$@"
fixgaps() {
local CMD="java $EA $EOOM $z -cp $CP consensus.FixScaffoldGaps $@"
echo $CMD >&2
eval $CMD
}
fixgaps "$@"
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