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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified July 27, 2015
Description: Maps reads, then filters an assembly by contig coverage.
Intended to reduce misassembly rate of SPAdes by removing suspicious contigs.
Usage: postfilter.sh in=<reads> ref=<contigs> out=<filtered contigs>
Standard Parameters:
in=<file> File containing input reads.
in2=<file> Optional file containing read mates.
ref=<file> File containing input assembly.
cov=covstats.txt File to write coverage stats generated by pileup.
out=filtered.fa Destination of clean output assembly.
outdirty=<file> (outd) Destination of removed contigs; optional.
ow=f (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).
int=f (interleaved) Determines whether input reads are considered interleaved.
Filtering Parameters:
minc=2 (mincov) Discard contigs with lower average coverage.
minp=95 (minpercent) Discard contigs with a lower percent covered bases.
minr=6 (minreads) Discard contigs with fewer mapped reads.
minl=400 (minlength) Discard shorter contigs.
trim=0 (trimends) Trim the first and last X bases of each sequence.
Mapping Parameters (unlisted params will use BBMap defaults)
minhits=2
maxindel=0
tipsearch=0
bw=20
rescue=f
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.
Other parameters will be passed directly to BBMap.
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 postfilter() {
local CMD="java $EA $EOOM $z -cp $CP assemble.Postfilter $@"
echo $CMD >&2
eval $CMD
}
postfilter "$@"
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