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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified February 17, 2015
Description: Generates fake read pairs from ends of contigs or single reads.
Usage: bbfakereads.sh in=<file> out=<outfile> out2=<outfile2>
Out2 is optional; if there is only one output file, it will be written interleaved.
Standard parameters:
ow=f (overwrite) Overwrites files that already exist.
zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
fastawrap=100 Length of lines in fasta output.
tuc=f (touppercase) Change lowercase letters in reads to uppercase.
qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
qfin=<.qual file> Read qualities from this qual file, for the reads coming from 'in=<fasta file>'
qfout=<.qual file> Write qualities from this qual file, for the reads going to 'out=<fasta file>'
qfout2=<.qual file> Write qualities from this qual file, for the reads coming from 'out2=<fasta file>'
verifyinterleaved=f (vint) When true, checks a file to see if the names look paired. Prints an error message if not.
tossbrokenreads=f (tbr) Discard reads that have different numbers of bases and qualities. By default this will be detected and cause a crash.
Faking parameters:
length=250 Generate reads of this length.
minlength=1 Don't generate reads shorter than this.
overlap=0 If you set overlap, then reads will by variable length, overlapping by 'overlap' in the middle.
identifier=null (id) Output read names are prefixed with this.
addspace=t Set to false to omit the space before /1 and /2 of paired reads.
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="-Xmx600m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
function fakereads() {
local CMD="java $EA $EOOM $z -cp $CP jgi.FakeReads $@"
echo $CMD >&2
eval $CMD
}
fakereads "$@"
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