--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/mergeribo.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,100 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified January 28, 2020
+
+Description:  Merges files of SSU sequences to keep one per taxID.
+By default, a consensus is generated per TaxID, then the sequence
+best matching that consensus is used:
+First, all sequences per TaxID are aligned to a reference consensus.
+Second, the best-matching sequence is used as a seed, and all other
+sequences for that TaxID are aligned to the seed to generate a new consensus.
+Third, in 'consensus' mode, that consensus is simply output.
+In 'best' mode (default), all sequences are aligned again to the new consensus,
+and the best-matching is output.
+
+Usage:  mergeribo.sh in=<file,file> out=<file> 16S
+
+Standard parameters:
+in=<file,file>  Comma-delimited list of files.
+out=<file>      Output file.
+out2=<file>     Read 2 output if reads are in two files.
+overwrite=f     (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.
+ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression
+                level; lower compression is faster.
+
+Processing parameters:
+alt=<file>      Lower priority data.  Only used if there is no SSU associated
+                with the TaxID from the primary input.
+best=t          Output the best representative per taxID.
+consensus=f     Output a consensus per taxID instead of the best input
+                sequence.  Mutually exclusive with best.
+fast=f          Output the best sequence based on alignment to global consensus
+                (the seed) rather than individual consensus.
+minid=0.62      Ignore sequences with identity lower than this to the global
+                consensus.
+maxns=-1        Ignore sequences with more than this many Ns, if non-negative.
+minlen=1        Ignore sequences shorter than this.
+maxlen=4000     Ignore sequences longer than this.
+16S=t           Align to 16S consensus to pick the seed. Mutually exclusive.
+18S=f           Align to 18S consensus to pick the seed. Mutually exclusive.
+
+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="-Xmx4g"
+z2="-Xms4g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 4000m 42
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+mergeribo() {
+	local CMD="java $EA $EOOM $z -cp $CP prok.MergeRibo $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+mergeribo "$@"