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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified February 17, 2015
Description: Separates paired reads into files of 'good' pairs and 'good' singletons by removing 'bad' reads that are shorter than a min length.
Designed to handle situations where reads become too short to be useful after trimming. This program also optionally performs quality trimming.
Usage: bbsplitpairs.sh in=<input file> out=<pair output file> outs=<singleton output file> minlen=<minimum read length, an integer>
Input may be fasta or fastq, compressed or uncompressed.
Optional parameters (and their defaults)
in=<file> The 'in=' flag is needed if the input file is not the first parameter. 'in=stdin' will pipe from standard in.
in2=<file> Use this if 2nd read of pairs are in a different file.
out=<file> The 'out=' flag is needed if the output file is not the second parameter. 'out=stdout' will pipe to standard out.
out2=<file> Use this to write 2nd read of pairs to a different file.
outsingle=<file> (outs) Write singleton reads here.
overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file.
showspeed=t (ss) Set to 'f' to suppress display of processing speed.
interleaved=auto (int) If true, forces fastq input to be paired and interleaved.
qtrim=f Trim read ends to remove bases with quality below trimq.
Values: rl (trim both ends), f (neither end), r (right end only), l (left end only).
trimq=6 Trim quality threshold.
minlen=20 (ml) Reads shorter than this after trimming will be discarded.
ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
fixinterleaving=f (fint) Fixes corrupted interleaved files by examining pair names. Only use on files with broken interleaving.
repair=f (rp) Fixes arbitrarily corrupted paired reads by examining read names. High memory.
ain=f (allowidenticalnames) When detecting pair names, allows identical names, instead of requiring /1 and /2 or 1: and 2:
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="-Xmx200m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
splitpairs() {
local CMD="java $EA $EOOM $z -cp $CP jgi.SplitPairsAndSingles $@"
echo $CMD >&2
eval $CMD
}
splitpairs "$@"
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