--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/decontaminate.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,128 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell.
+Last modified June 28, 2016
+
+Description:  Decontaminates multiplexed assemblies via normalization and mapping.
+
+Usage:  decontaminate.sh reads=<file,file> ref=<file,file> out=<directory>
+or
+decontaminate.sh readnamefile=<file> refnamefile=<file> out=<directory>
+
+Input Parameters:
+reads=<file,file>   Input reads, one file per library.
+ref=<file,file>     Input assemblies, one file per library.
+readnamefile=<file> List of input reads, one line per library.
+refnamefile=<file>  List of input assemblies, one line per library.
+
+interleaved=auto    True forces paired/interleaved input; false forces single-ended mapping.
+                    If not specified, interleaved status will be autodetected from read names.
+unpigz=t            Spawn a pigz (parallel gzip) process for faster decompression.  Requires pigz to be installed.
+touppercase=t       (tuc) Convert lowercase letters in reads to upper case (otherwise they will not match the reference).
+
+Output Parameters:
+pigz=f              Spawn a pigz (parallel gzip) process for faster compression.  Requires pigz to be installed.
+tmpdir=.            Write temp files here.  By default is uses the system's $TMPDIR or current directory.
+outdir=.            Write ouput files here.
+
+Mapping Parameters:
+kfilter=55          Set to a positive number N to require minimum N contiguous matches for a mapped read.
+ambig=random        Determines how coverage will be calculated for ambiguously-mapped reads.
+                        first: Add coverage only at first genomic mapping location.
+                        random: Add coverage at a random best-scoring location.
+                        all: Add coverage at all best-scoring locations.
+                        toss: Discard ambiguously-mapped reads without adding coverage.
+
+Filtering Parameters:
+minc=3.5            Min average coverage to retain scaffold.
+minp=20             Min percent coverage to retain scaffold.
+minr=18             Min mapped reads to retain scaffold.
+minl=500            Min length to retain scaffold.
+ratio=1.2           Contigs will not be removed by minc unless the coverage changed by at least this factor.  0 disables this filter.
+mapraw=t            Set true to map the unnormalized reads.  Required to filter by 'ratio'.
+basesundermin=-1    If positive, removes contigs with at least this many bases in low-coverage windows.
+window=500          Sliding window size 
+windowcov=5         Average coverage below this will be classified as low.
+
+Tadpole Parameters:
+ecct=f              Error-correct with Tadpole before normalization.
+kt=42               Kmer length for Tadpole.
+aggressive=f        Do aggressive error correction.
+conservative=f      Do conservative error correction.
+tadpoleprefilter=1  (tadpre) Ignore kmers under this depth to save memory.
+
+Normalization Parameters:
+mindepth=2          Min depth of reads to keep.
+target=20           Target normalization depth.
+hashes=4            Number of hashes in Bloom filter.
+passes=1            Normalization passes.
+minprob=0.5         Min probability of correctness to add a kmer.
+dp=0.75             (depthpercentile) Percentile to use for depth proxy (0.5 means median).
+prefilter=t         Prefilter, for large datasets.
+filterbits=32       (fbits) Bits per cell in primary filter.
+prefilterbits=2     (pbits) Bits per cell in prefilter.
+k=31                Kmer length for normalization.  Longer is more precise but less sensitive.
+
+Other parameters:
+opfn=0              (onlyprocessfirstn) Set to a positive number to only process that many datasets.  This is for internal testing of specificity.
+
+Java Parameters:
+-Xmx                This will set Java's memory usage, overriding autodetection.
+                    -Xmx20g will specify 20 gigs of RAM, and -Xmx800m will specify 800 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="$DIR""current/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""
+
+z="-Xmx1g"
+z2="-Xms1g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 15000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+
+decontaminate() {
+	local CMD="java $JNI $EA $EOOM $z $z2 -cp $CP jgi.DecontaminateByNormalization $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+decontaminate "$@"