--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/addadapters.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,78 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified February 17, 2015
+
+***DEPRECATED***
+
+Description:  Randomly adds adapters to a file, or grades a trimmed file.
+The input is a set of reads, paired or unpaired.
+The output is those same reads with adapter sequence replacing some of the bases in some reads.
+For paired reads, adapters are located in the same position in read1 and read2.
+This is designed for benchmarking adapter-trimming software, and evaluating methodology.
+randomreads.sh is better for paired reads, though, as it actually adds adapters at the correct location,
+so that overlap may be used for adapter detection.
+
+Usage:  addadapters.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> adapters=<file>
+
+in2 and out2 are for paired reads and are optional.
+If input is paired and there is only one output file, it will be written interleaved.
+
+Parameters:
+ow=f                (overwrite) Overwrites files that already exist.
+int=f               (interleaved) Determines whether INPUT file is considered interleaved.
+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).
+add                 Add adapters to input files.  Default mode.
+grade               Evaluate trimmed input files.
+adapters=<file>     Fasta file of adapter sequences.
+literal=<sequence>  Comma-delimited list of adapter sequences.
+left                Adapters are on the left (3') end of the read.
+right               Adapters are on the right (5') end of the read.  Default mode.
+adderrors=t         Add errors to adapters based on the quality scores.
+addpaired=t         Add adapters to the same location for read 1 and read 2.
+arc=f               Add reverse-complemented adapters as well as forward.
+rate=0.5            Add adapters to this fraction of reads.
+
+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 "$@"
+}
+calcXmx "$@"
+
+function addadapters() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.AddAdapters $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+addadapters "$@"