--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/rename.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,94 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified April 1, 2020
+
+Description:  Renames reads to <prefix>_<number> where you specify the prefix
+and the numbers are ordered.  There are other renaming modes too.
+If reads are paired, pairs should be processed together; if reads are 
+interleaved, the interleaved flag should be set.  This ensures that if a
+read number (such as 1: or 2:) is added, it will be added correctly.
+
+Usage:  rename.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> prefix=<>
+
+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:
+prefix=             The string to prepend to existing read names.
+ow=f                (overwrite) Overwrites files that already exist.
+zl=4                (ziplevel) Set compression level, 1 (low) to 9 (max).
+int=f               (interleaved) Determines whether INPUT file is considered interleaved.
+fastawrap=70        Length of lines in fasta output.
+minscaf=1           Ignore fasta reads shorter than this.
+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).
+ignorebadquality=f  (ibq) Fix out-of-range quality values instead of crashing with a warning.
+
+Renaming modes (if not default):
+renamebyinsert=f    Rename the read to indicate its correct insert size.
+renamebymapping=f   Rename the read to indicate its correct mapping coordinates.
+renamebytrim=f      Rename the read to indicate its correct post-trimming length.
+addprefix=f         Rename the read by prepending the prefix to the existing name.
+prefixonly=f        Only use the prefix; don't add _<number>
+addunderscore=t     Add an underscore after the prefix (if there is a prefix).
+addpairnum=t        Add a pairnum (e.g. ' 1:') to paired reads in some modes.
+fixsra=f            Fixes headers of SRA reads renamed from Illumina.
+                    Specifically, it converts something like this:
+                    SRR17611.11 HWI-ST79:17:D091UACXX:4:1101:210:824 length=75
+                    ...into this:
+                    HWI-ST79:17:D091UACXX:4:1101:210:824 1:
+
+Sampling parameters:
+reads=-1            Set to a positive number to only process this many INPUT reads (or pairs), then quit.
+
+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="-Xmx1g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+function rename() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.RenameReads $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+rename "$@"