--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/summarizeseal.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,74 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified June 22, 2016
+
+Description:  Summarizes the stats output of Seal for evaluation of 
+cross-contamination.  The intended use is to map multiple libraries or 
+assemblies, of different multiplexed organisms, to a concatenated reference 
+containing one fused scaffold per organism.  This will convert all of the 
+resulting stats files (one per library) to a single text file, with multiple 
+columns, indicating how much of the input hit the primary versus nonprimary 
+scaffolds.
+
+If ingoresametaxa or ignoresamebarcode are used, ref names must be 
+in this format:
+barcode,library,tax,location
+For example:
+6-G,N0296,gammaproteobacteria_bacterium,deep_ocean
+
+Usage:  summarizeseal.sh in=<file,file...> out=<file>
+
+You can alternately run 'summarizeseal.sh *.txt out=out.txt'
+
+Parameters:
+in=<file>              A list of stats files, or a text file containing one stats file name per line.
+out=<file>             Destination for summary.
+printtotal=t           (pt) Print a line summarizing the total contamination rate of all assemblies.
+ignoresametaxa=f       Ignore secondary hits sharing taxonomy. 
+ignoresamebarcode=f    Ignore secondary hits sharing a barcode.
+ignoresamelocation=f   Ignore secondary hits sharing a sampling site.
+totaldenominator=f     (td) Use all bases as denominator rather than mapped bases.
+
+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="-Xmx120m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+summarizeseal() {
+	local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeSealStats $@"
+#	echo $CMD >&2
+	eval $CMD
+}
+
+summarizeseal "$@"