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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified May 3, 2016
Description: Filters an assembly by contig coverage.
The coverage stats file can be generated by BBMap or Pileup.
Usage: filterbycoverage.sh in=<assembly> cov=<coverage stats> out=<filtered assembly> mincov=5
Parameters:
in=<file> File containing input assembly.
cov=<file> File containing coverage stats generated by pileup.
cov0=<file> Optional file containing coverage stats before normalization.
out=<file> Destination of clean output assembly.
outd=<file> (outdirty) Destination of dirty output containing only removed contigs.
minc=5 (mincov) Discard contigs with lower average coverage.
minp=40 (minpercent) Discard contigs with a lower percent covered bases.
minr=0 (minreads) Discard contigs with fewer mapped reads.
minl=1 (minlength) Discard contigs shorter than this (after trimming).
trim=0 (trimends) Trim the first and last X bases of each sequence.
ratio=0 If cov0 is set, contigs will not be removed unless the coverage ratio (of cov to cov0) is at least this (0 disables it).
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).
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 filterbycoverage() {
local CMD="java $EA $EOOM $z -cp $CP jgi.FilterByCoverage $@"
echo $CMD >&2
eval $CMD
}
filterbycoverage "$@"
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