--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/comparesketch.sh	Tue Mar 18 17:55:14 2025 -0400
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+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified Jan 7, 2020
+
+Description:  Compares query sketches to others, and prints their kmer identity.
+The input can be sketches made by sketch.sh, or fasta/fastq files.
+It's recommended to first sketch references with sketch.sh for large files,
+or when taxonomic information is desired.
+
+Please read bbmap/docs/guides/BBSketchGuide.txt for more information.
+
+Usage:  comparesketch.sh in=<file,file,file...> ref=<file,file,file...>
+Alternative:  comparesketch.sh in=<file,file,file...> file file file
+Alternative:  comparesketch.sh in=<file,file,file...> *.sketch
+Alternative:  comparesketch.sh alltoall *.sketch.gz
+
+File parameters:
+in=<file,file...>   Sketches or fasta files to compare.
+out=stdout          Comparison output.  Can be set to a file instead.
+outsketch=<file>    Optionally write sketch files generated from the input.
+ref=<file,file...>  List of sketches to compare against.  Files given without
+                    a prefix (ref=) will be treated as references,
+                    so you can use *.sketch without ref=.
+                    You can also do ref=nt#.sketch to load all numbered files
+                    fitting that pattern.
+                    On NERSC, you can use these abbreviations (e.g. ref=nt):
+                       nt:      nt sketches
+                       refseq:  Refseq sketches
+                       silva:   Silva sketches
+                       img:     IMG sketches
+                       mito:    RefSeq mitochondrial sketches
+                       fungi:   RefSeq fungi sketches
+                       protein: RefSeq prokaryotic amino acid sketches
+                    Using an abbreviation automatically sets the blacklist, 
+                    and k.  If the reference is in amino space, the query
+                    also be in amino acid space with the flag amino added.
+                    If the query is in nucleotide space, use the flag
+                    'translate', but this will only work for prokaryotes.
+
+Blacklist and Whitelist parameters:
+blacklist=<file>    Ignore keys in this sketch file.  Additionally, 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
+whitelist=f         Ignore keys that are not in the index.  Requires index=t.
+
+Sketch-making parameters:
+mode=perfile        Possible modes, for sequence input:
+                       single: Generate one sketch.
+                       sequence: Generate one sketch per sequence.
+                       perfile: Generate one sketch per file.
+sketchonly=f        Don't run comparisons, just write the output sketch file.
+k=31                Kmer length, 1-32.  To maximize sensitivity and 
+                    specificity, dual kmer lengths may be used:  k=31,24
+                    Dual kmers are fastest if the shorter is a multiple 
+                    of 4.  Query and reference k must match.
+samplerate=1        Set to a lower value to sample a fraction of input reads.
+                    For raw reads (rather than an assembly), 1-3x coverage
+                    gives best results, by reducing error kmers.  Somewhat
+                    higher is better for high-error-rate data like PacBio.
+minkeycount=1       Ignore kmers that occur fewer times than this.  Values
+                    over 1 can be used with raw reads to avoid error kmers.
+minprob=0.0001      Ignore kmers below this probability of correctness.
+minqual=0           Ignore kmers spanning bases below this quality.
+entropy=0.66        Ignore sequence with entropy below this value.
+merge=f             Merge paired reads prior to sketching.
+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.
+sixframes=f         Translate all 6 frames instead of predicting genes.
+ssu=t               Scan for and retain full-length SSU sequence.
+printssusequence=f  Print the query SSU sequence (JSON mode only).
+
+Size parameters:
+size=10000          Desired size of sketches (if not using autosize).
+mgf=0.01            (maxfraction) 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.
+sketchheapfactor=4  If minkeycount>1, temporarily track this many kmers until
+                    counts are known and low-count kmers are discarded.
+
+Sketch comparing parameters:
+threads=auto        Use this many threads for comparison.
+index=auto          Index the sketches for much faster searching.
+                    Requires more memory and adds startup time.
+                    Recommended true for many query sketches, false for few.
+prealloc=f          Preallocate the index for greater efficiency.
+                    Can be set to a number between 0 and 1 to determine how 
+                    much of total memory should be used.
+alltoall            (ata) Compare all refs to all.  Must be sketches.
+compareself=f       In all-to-all mode, compare a sketch to itself.
+
+Taxonomy-related parameters:
+tree=<file>         Specify a TaxTree file.  On Genepool, use tree=auto.
+                    Only necessary for use with printtaxa and level.
+                    Assumes comparisons are done against reference sketches
+                    with known taxonomy information.
+level=2             Only report the best record per taxa at this level.
+                    Either level names or numbers may be used.
+                        0: disabled
+                        1: subspecies
+                        2: species
+                        3: genus
+                       ...etc
+include=            Restrict output to organisms in these clades.
+                    May be a comma-delimited list of names or NCBI TaxIDs.
+includelevel=0      Promote the include list to this taxonomic level.
+                    For example, include=h.sapiens includelevel=phylum
+                    would only include organisms in the same phylum as human.
+includestring=      Only report records whose name contains this string.
+exclude=            Ignore organisms in these clades.
+                    May be a comma-delimited list of names or NCBI TaxIDs.
+excludelevel=0      Promote the exclude list to this taxonomic level.
+                    For example, exclude=h.sapiens excludelevel=phylum
+                    would exclude all organisms in the same phylum as human.
+excludestring=      Do not records whose name contains this string.
+minlevel=           Use this to restrict comparisons to distantly-related
+                    organisms.  Intended for finding misclassified organisms
+                    using all-to-all comparisons.  minlevel=order would only
+                    report hits between organisms related at the order level
+                    or higher, not between same species or genus.
+banunclassified=f   Ignore organisms descending from nodes like 
+                    'unclassified Bacteria'
+banvirus=f          Ignore viruses.
+requiressu=f        Ignore records without SSUs.
+minrefsize=0        Ignore ref sketches smaller than this (unique kmers).
+minrefsizebases=0   Ignore ref sketches smaller than this (total base pairs).
+
+Output format:
+format=2            2: Default format with, per query, one query header line;
+                       one column header line; and one reference line per hit.
+                    3: One line per hit, with columns query, reference, ANI,
+                       and sizeRatio. Useful for all-to-all comparisons.
+                    4: JSON (format=json also works).
+                    5: Constellation (format=constellation also works).
+usetaxidname=f      For format 3, print the taxID in the name column.
+usetaxname          for format 3, print the taxonomic name in the name column.
+useimgname          For format 3, print the img ID in the name column.
+
+Output columns (for format=2):
+printall=f          Enable all output columns.
+printani=t          (ani) Print average nucleotide identity estimate.
+completeness=t      Genome completeness estimate.
+score=f             Score (used for sorting the output).
+printmatches=t      Number of kmer matches to reference.
+printlength=f       Number of kmers compared.
+printtaxid=t        NCBI taxID.
+printimg=f          IMG identifier (only for IMG data).
+printgbases=f       Number of genomic bases.
+printgkmers=f       Number of genomic kmers.
+printgsize=t        Estimated number of unique genomic kmers.
+printgseqs=t        Number of sequences (scaffolds/reads).
+printtaxname=t      Name associated with this taxID.
+printname0=f        (pn0) Original seqeuence name.
+printfname=t        Query filename.
+printtaxa=f         Full taxonomy of each record.
+printcontam=t       Print contamination estimate, and factor contaminant kmers
+                    into calculations.  Kmers are considered contaminant if
+                    present in some ref sketch but not the current one.
+printunique=t       Number of matches unique to this reference.
+printunique2=f      Number of matches unique to this reference's taxa.
+printunique3=f      Number of query kmers unique to this reference's taxa,
+                    regardless of whether they are in this reference sketch.
+printnohit=f        Number of kmers that don't hit anything.
+printrefhits=f      Average number of ref sketches hit by shared kmers.
+printgc=f           GC content.
+printucontam=f      Contam hits that hit exactly one reference sketch.
+printcontam2=f      Print contamination estimate using only kmer hits
+                    to unrelated taxa.
+contamlevel=species Taxonomic level to use for contam2/unique2/unique3.
+NOTE: unique2/unique3/contam2/refhits require an index.
+
+printdepth=f        (depth) Print average depth of sketch kmers; intended
+                    for shotgun read input.
+printdepth2=f       (depth2) Print depth compensating for genomic repeats.
+                    Requires reference sketches to be generated with depth.
+actualdepth=t       If this is false, the raw average count is printed.
+                    If true, the raw average (observed depth) is converted 
+                    to estimated actual depth (including uncovered areas).
+printvolume=f       (volume) Product of average depth and matches.
+printca=f           Print common ancestor, if query taxID is known.
+printcal=f          Print common ancestor tax level, if query taxID is known.
+recordsperlevel=0   If query TaxID is known, and this is positive, print this
+                    many records per common ancestor level.
+
+Sorting:
+sortbyscore=t       Default sort order is by score, a composite metric.
+sortbydepth=f       Include depth as a factor in sort order.
+sortbydepth2=f      Include depth2 as a factor in sort order.
+sortbyvolume=f      Include volume as a factor in sort order.
+sortbykid=f         Sort strictly by KID.
+sortbyani=f         Sort strictly by ANI/AAI/WKID.
+sortbyhits=f        Sort strictly by the number of kmer hits.
+
+Other output parameters:
+minhits=3           (hits) Only report records with at least this many hits.
+minani=0            (ani) Only report records with at least this ANI (0-1).
+minwkid=0.0001      (wkid) Only report records with at least this WKID (0-1).
+anifromwkid=t       Calculate ani from wkid.  If false, use kid.
+minbases=0          Ignore ref sketches of sequences shortert than this.
+minsizeratio=0      Don't compare sketches if the smaller genome is less than
+                    this fraction of the size of the larger.
+records=20          Report at most this many best-matching records.
+color=family        Color records at the family level.  color=f will disable.
+                    Colors work in most terminals but may cause odd characters
+                    to appear in text editors.  So, color defaults to f if 
+                    writing to a file.  Requires the taxtree to be loaded.
+intersect=f         Print sketch intersections.  delta=f is suggested.
+
+Metadata flags (optional, for the query sketch header):
+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.
+
+Other parameters:
+requiredmeta=       (rmeta) Required optional metadata values.  For example:
+                    rmeta=subunit:ssu,source:silva
+bannedmeta=         (bmeta) Forbidden optional metadata values.
+
+
+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 [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 3200m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+comparesketch() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP sketch.CompareSketch $@"
+#	echo $CMD >&2
+	eval $CMD
+}
+
+comparesketch "$@"