--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbfakereads.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,82 @@
+#!/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 $CMD
+}
+
+fakereads "$@"