--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/dedupe.sh	Tue Mar 18 17:55:14 2025 -0400
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+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell and Jonathan Rood
+Last modified February 19, 2020
+
+Description:  Accepts one or more files containing sets of sequences (reads or scaffolds).
+Removes duplicate sequences, which may be specified to be exact matches, subsequences, or sequences within some percent identity.
+Can also find overlapping sequences and group them into clusters.
+Please read bbmap/docs/guides/DedupeGuide.txt for more information.
+
+Usage:     dedupe.sh in=<file or stdin> out=<file or stdout>
+
+An example of running Dedupe for clustering short reads:
+dedupe.sh in=x.fq am=f ac=f fo c pc rnc=f mcs=4 mo=100 s=1 pto cc qin=33 csf=stats.txt pattern=cluster_%.fq dot=graph.dot
+
+Input may be fasta or fastq, compressed or uncompressed.
+Output may be stdout or a file.  With no output parameter, data will be written to stdout.
+If 'out=null', there will be no output, but statistics will still be printed.
+You can also use 'dedupe <infile> <outfile>' without the 'in=' and 'out='.
+
+I/O parameters:
+in=<file,file>        A single file or a comma-delimited list of files.
+out=<file>            Destination for all output contigs.
+pattern=<file>        Clusters will be written to individual files, where the '%' symbol in the pattern is replaced by cluster number.
+outd=<file>           Optional; removed duplicates will go here.
+csf=<file>            (clusterstatsfile) Write a list of cluster names and sizes.
+dot=<file>            (graph) Write a graph in dot format.  Requires 'fo' and 'pc' flags.
+threads=auto          (t) Set number of threads to use; default is number of logical processors.
+overwrite=t           (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.
+minscaf=0             (ms) Ignore contigs/scaffolds shorter than this.
+interleaved=auto      If true, forces fastq input to be paired and interleaved.
+ziplevel=2            Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
+
+Output format parameters:
+storename=t           (sn) Store scaffold names (set false to save memory).
+#addpairnum=f         Add .1 and .2 to numeric id of read1 and read2.
+storequality=t        (sq) Store quality values for fastq assemblies (set false to save memory).
+uniquenames=t         (un) Ensure all output scaffolds have unique names.  Uses more memory.
+mergenames=f          When a sequence absorbs another, concatenate their headers.
+mergedelimiter=>      Delimiter between merged headers.  Can be a symbol name like greaterthan.
+numbergraphnodes=t    (ngn) Label dot graph nodes with read numbers rather than read names.
+sort=f                Sort output (otherwise it will be random).  Options:
+                         length:  Sort by length
+                         quality: Sort by quality
+                         name:    Sort by name
+                         id:      Sort by input order
+ascending=f           Sort in ascending order.
+ordered=f             Output sequences in input order.  Equivalent to sort=id ascending.
+renameclusters=f      (rnc) Rename contigs to indicate which cluster they are in.
+printlengthinedges=f  (ple) Print the length of contigs in edges.
+
+Processing parameters:
+absorbrc=t            (arc) Absorb reverse-complements as well as normal orientation.
+absorbmatch=t         (am) Absorb exact matches of contigs.
+absorbcontainment=t   (ac) Absorb full containments of contigs.
+#absorboverlap=f      (ao) Absorb (merge) non-contained overlaps of contigs (TODO).
+findoverlap=f         (fo) Find overlaps between contigs (containments and non-containments).  Necessary for clustering.
+uniqueonly=f          (uo) If true, all copies of duplicate reads will be discarded, rather than keeping 1.
+rmn=f                 (requirematchingnames) If true, both names and sequence must match.
+usejni=f              (jni) Do alignments in C code, which is faster, if an edit distance is allowed.
+                      This will require compiling the C code; details are in /jni/README.txt.
+
+Subset parameters:
+subsetcount=1         (sstc) Number of subsets used to process the data; higher uses less memory.
+subset=0              (sst) Only process reads whose ((ID%subsetcount)==subset).
+
+Clustering parameters:
+cluster=f             (c) Group overlapping contigs into clusters.
+pto=f                 (preventtransitiveoverlaps) Do not look for new edges between nodes in the same cluster.
+minclustersize=1      (mcs) Do not output clusters smaller than this.
+pbr=f                 (pickbestrepresentative) Only output the single highest-quality read per cluster.
+
+Cluster postprocessing parameters:
+processclusters=f     (pc) Run the cluster processing phase, which performs the selected operations in this category.
+                      For example, pc AND cc must be enabled to perform cc.
+fixmultijoins=t       (fmj) Remove redundant overlaps between the same two contigs.
+removecycles=t        (rc) Remove all cycles so clusters form trees.
+cc=t                  (canonicizeclusters) Flip contigs so clusters have a single orientation.
+fcc=f                 (fixcanoncontradictions) Truncate graph at nodes with canonization disputes.
+foc=f                 (fixoffsetcontradictions) Truncate graph at nodes with offset disputes.
+mst=f                 (maxspanningtree) Remove cyclic edges, leaving only the longest edges that form a tree.
+
+Overlap Detection Parameters
+exact=t               (ex) Only allow exact symbol matches.  When false, an 'N' will match any symbol.
+touppercase=t         (tuc) Convert input bases to upper-case; otherwise, lower-case will not match.
+maxsubs=0             (s) Allow up to this many mismatches (substitutions only, no indels).  May be set higher than maxedits.
+maxedits=0            (e) Allow up to this many edits (subs or indels).  Higher is slower.
+minidentity=100       (mid) Absorb contained sequences with percent identity of at least this (includes indels).
+minlengthpercent=0    (mlp) Smaller contig must be at least this percent of larger contig's length to be absorbed.
+minoverlappercent=0   (mop) Overlap must be at least this percent of smaller contig's length to cluster and merge.
+minoverlap=200        (mo) Overlap must be at least this long to cluster and merge.
+depthratio=0          (dr) When non-zero, overlaps will only be formed between reads with a depth ratio of at most this.
+                      Should be above 1.  Depth is determined by parsing the read names; this information can be added
+                      by running KmerNormalize (khist.sh, bbnorm.sh, or ecc.sh) with the flag 'rename'
+k=31                  Seed length used for finding containments and overlaps.  Anything shorter than k will not be found.
+numaffixmaps=1        (nam) Number of prefixes/suffixes to index per contig. Higher is more sensitive, if edits are allowed.
+hashns=f              Set to true to search for matches using kmers containing Ns.  Can lead to extreme slowdown in some cases.
+#ignoreaffix1=f       (ia1) Ignore first affix (for testing).
+#storesuffix=f        (ss) Store suffix as well as prefix.  Automatically set to true when doing inexact matches.
+
+Other Parameters
+qtrim=f               Set to qtrim=rl to trim leading and trailing Ns.
+trimq=6               Quality trim level.
+forcetrimleft=-1      (ftl) If positive, trim bases to the left of this position (exclusive, 0-based).
+forcetrimright=-1     (ftr) If positive, trim bases to the right of this position (exclusive, 0-based).
+
+Note on Proteins / Amino Acids
+Dedupe supports amino acid space via the 'amino' flag.  This also changes the default kmer length to 10.
+In amino acid mode, all flags related to canonicity and reverse-complementation are disabled,
+and nam (numaffixmaps) is currently limited to 2 per tip.
+
+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/"
+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 [[ $set == 1 ]]; then
+	return
+	fi
+	freeRam 3200m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+dedupe() {
+	local CMD="java $JNI $EA $EOOM $z $z2 -cp $CP jgi.Dedupe $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+dedupe "$@"