--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/sketch.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,156 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified January 28, 2020
+
+Description:  Creates one or more sketches from a fasta file,
+optionally annotated with taxonomic information.
+
+Please read bbmap/docs/guides/BBSketchGuide.txt for more information.
+
+Usage:  sketch.sh in=<fasta file> out=<sketch file>
+
+Standard parameters:
+in=<file>           A fasta file containing one or more sequences.
+out=<file>          Output filename.  If multiple files are desired it must
+                    contain the # symbol.
+blacklist=<file>    Ignore keys in this sketch file.  Additionaly, there are
+                    built-in blacklists that can be specified:
+                       nt:      Blacklist for nt
+                       refseq:  Blacklist for Refseq
+                       silva:   Blacklist for Silva
+                       img:     Blacklist for IMG
+files=1             Number of output sketch files to produce, for parallel 
+                    loading.  Independent of the number of sketches produced; 
+                    sketches will be randomly distributed between files.
+k=32,24             Kmer length, 1-32.  To maximize sensitivity and 
+                    specificity, dual kmer lengths may be used, e.g. k=32,24
+                    Query and reference k must match.
+rcomp=t             Look at reverse-complement kmers also.
+amino=f             Use amino acid mode.  Input should be amino acids.
+translate=f         Call genes and translate to proteins.  Input should be
+                    nucleotides.  Designed for prokaryotes.
+mode=single         Possible modes:
+                       single: Write one sketch.
+                       sequence: Write one sketch per sequence.
+                       taxa: Write one sketch per taxonomic unit.
+                          Requires more memory, and taxonomic annotation.
+                       img: Write one sketch per IMG id.
+delta=t             Delta-compress sketches.
+a48=t               Encode sketches as ASCII-48 rather than hex.
+depth=f             Track the number of times kmers appear.
+                    Required for the depth2 field in comparisons.
+entropy=0.66        Ignore sequence with entropy below this value.
+ssu=t               Scan for and retain full-length SSU sequence.
+
+Size parameters:
+size=10000          Desired size of sketches (if not using autosize).
+maxfraction=0.01    (mgf) Max fraction of genomic kmers to use.
+minsize=100         Do not generate sketches for genomes smaller than this.
+autosize=t          Use flexible sizing instead of fixed-length.  This is
+                    nonlinear; a human sketch is only ~6x a bacterial sketch.
+sizemult=1          Multiply the autosized size of sketches by this factor.
+                    Normally a bacterial-size genome will get a sketch size
+                    of around 10000; if autosizefactor=2, it would be ~20000.
+density=            If this flag is set (to a number between 0 and 1),
+                    autosize and sizemult are ignored, and this fraction of
+                    genomic kmers are used.  For example, at density=0.001,
+                    a 4.5Mbp bacteria will get a 4500-kmer sketch.
+
+Metadata flags (optional; intended for single-sketch mode):
+taxid=-1            Set the NCBI taxid.
+imgid=-1            Set the IMG id.
+spid=-1             Set the JGI sequencing project id.
+name=               Set the name (taxname).
+name0=              Set name0 (normally the first sequence header).
+fname=              Set fname (normally the file name).
+meta_=              Set an arbitrary metadata field.
+                    For example, meta_Month=March.
+
+Taxonomy-specific flags:
+tree=               Specify a taxtree file.  On Genepool, use 'auto'.
+gi=                 Specify a gitable file.  On Genepool, use 'auto'.
+accession=          Specify one or more comma-delimited NCBI accession to
+                    taxid files.  On Genepool, use 'auto'.
+imgdump=            Specify an IMG dump file containing NCBI taxIDs,
+                    for IMG mode.
+taxlevel=subspecies Taxa hits below this rank will be promoted and merged
+                    with others.
+prefilter=f         For huge datasets full of junk like nt, this flag
+                    will save memory by ignoring taxa smaller than minsize.
+                    Requires taxonomic information (tree and gi).
+tossjunk=t          For taxa mode, discard taxonomically uninformative
+                    sequences.  This includes sequences with no taxid,
+                    with a tax level NO_RANK, of parent taxid of LIFE.
+silva=f             Parse headers using Silva or semicolon-delimited syntax.
+
+Ribosomal flags, which allow SSU sequences to be attached to sketches:
+processSSU=t        Run gene-calling to detect ribosomal SSU sequences.
+16Sfile=<file>      Optional file of 16S sequences, annotated with TaxIDs.
+18Sfile=<file>      Optional file of 18S sequences, annotated with TaxIDs.
+preferSSUMap=f      Prefer file SSUs over called SSUs.
+preferSSUMapEuks=t  Prefer file SSUs over called SSUs for Eukaryotes.
+SSUMapOnly=f        Only use file SSUs.
+SSUMapOnlyEuks=f    Only use file SSUs for Eukaryotes.  This prevents
+                    associating an organism with its mitochondrial or
+                    chloroplast 16S/18S, which is otherwise a problem.
+
+
+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.
+
+For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
+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 [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 4000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+sketch() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP sketch.SketchMaker $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+sketch "$@"