--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbduk.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,373 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified July 28, 2022
+
+Description:  Compares reads to the kmers in a reference dataset, optionally 
+allowing an edit distance. Splits the reads into two outputs - those that 
+match the reference, and those that don't. Can also trim (remove) the matching 
+parts of the reads rather than binning the reads.
+Please read bbmap/docs/guides/BBDukGuide.txt for more information.
+
+Usage:  bbduk.sh in=<input file> out=<output file> ref=<contaminant files>
+
+Input may be stdin or a fasta or fastq file, compressed or uncompressed.
+If you pipe via stdin/stdout, please include the file type; e.g. for gzipped 
+fasta input, set in=stdin.fa.gz
+
+Input parameters:
+in=<file>           Main input. in=stdin.fq will pipe from stdin.
+in2=<file>          Input for 2nd read of pairs in a different file.
+ref=<file,file>     Comma-delimited list of reference files.
+                    In addition to filenames, you may also use the keywords:
+                    adapters, artifacts, phix, lambda, pjet, mtst, kapa
+literal=<seq,seq>   Comma-delimited list of literal reference sequences.
+touppercase=f       (tuc) Change all bases upper-case.
+interleaved=auto    (int) t/f overrides interleaved autodetection.
+qin=auto            Input quality offset: 33 (Sanger), 64, or auto.
+reads=-1            If positive, quit after processing X reads or pairs.
+copyundefined=f     (cu) Process non-AGCT IUPAC reference bases by making all
+                    possible unambiguous copies.  Intended for short motifs
+                    or adapter barcodes, as time/memory use is exponential.
+samplerate=1        Set lower to only process a fraction of input reads.
+samref=<file>       Optional reference fasta for processing sam files.
+
+Output parameters:
+out=<file>          (outnonmatch) Write reads here that do not contain 
+                    kmers matching the database.  'out=stdout.fq' will pipe 
+                    to standard out.
+out2=<file>         (outnonmatch2) Use this to write 2nd read of pairs to a 
+                    different file.
+outm=<file>         (outmatch) Write reads here that fail filters.  In default
+                    kfilter mode, this means any read with a matching kmer.
+                    In any mode, it also includes reads that fail filters such
+                    as minlength, mingc, maxgc, entropy, etc.  In other words,
+                    it includes all reads that do not go to 'out'.
+outm2=<file>        (outmatch2) Use this to write 2nd read of pairs to a 
+                    different file.
+outs=<file>         (outsingle) Use this to write singleton reads whose mate 
+                    was trimmed shorter than minlen.
+stats=<file>        Write statistics about which contamininants were detected.
+refstats=<file>     Write statistics on a per-reference-file basis.
+rpkm=<file>         Write RPKM for each reference sequence (for RNA-seq).
+dump=<file>         Dump kmer tables to a file, in fasta format.
+duk=<file>          Write statistics in duk's format. *DEPRECATED*
+nzo=t               Only write statistics about ref sequences with nonzero hits.
+overwrite=t         (ow) Grant permission to overwrite files.
+showspeed=t         (ss) 'f' suppresses display of processing speed.
+ziplevel=2          (zl) Compression level; 1 (min) through 9 (max).
+fastawrap=70        Length of lines in fasta output.
+qout=auto           Output quality offset: 33 (Sanger), 64, or auto.
+statscolumns=3      (cols) Number of columns for stats output, 3 or 5.
+                    5 includes base counts.
+rename=f            Rename reads to indicate which sequences they matched.
+refnames=f          Use names of reference files rather than scaffold IDs.
+trd=f               Truncate read and ref names at the first whitespace.
+ordered=f           Set to true to output reads in same order as input.
+maxbasesout=-1      If positive, quit after writing approximately this many
+                    bases to out (outu/outnonmatch).
+maxbasesoutm=-1     If positive, quit after writing approximately this many
+                    bases to outm (outmatch).
+json=f              Print to screen in json format.
+
+Histogram output parameters:
+bhist=<file>        Base composition histogram by position.
+qhist=<file>        Quality histogram by position.
+qchist=<file>       Count of bases with each quality value.
+aqhist=<file>       Histogram of average read quality.
+bqhist=<file>       Quality histogram designed for box plots.
+lhist=<file>        Read length histogram.
+phist=<file>        Polymer length histogram.
+gchist=<file>       Read GC content histogram.
+enthist=<file>      Read entropy histogram.
+ihist=<file>        Insert size histogram, for paired reads in mapped sam.
+gcbins=100          Number gchist bins.  Set to 'auto' to use read length.
+maxhistlen=6000     Set an upper bound for histogram lengths; higher uses 
+                    more memory.  The default is 6000 for some histograms
+                    and 80000 for others.
+
+Histograms for mapped sam/bam files only:
+histbefore=t        Calculate histograms from reads before processing.
+ehist=<file>        Errors-per-read histogram.
+qahist=<file>       Quality accuracy histogram of error rates versus quality 
+                    score.
+indelhist=<file>    Indel length histogram.
+mhist=<file>        Histogram of match, sub, del, and ins rates by position.
+idhist=<file>       Histogram of read count versus percent identity.
+idbins=100          Number idhist bins.  Set to 'auto' to use read length.
+varfile=<file>      Ignore substitution errors listed in this file when 
+                    calculating error rates.  Can be generated with
+                    CallVariants.
+vcf=<file>          Ignore substitution errors listed in this VCF file 
+                    when calculating error rates.
+ignorevcfindels=t   Also ignore indels listed in the VCF.
+
+Processing parameters:
+k=27                Kmer length used for finding contaminants.  Contaminants 
+                    shorter than k will not be found.  k must be at least 1.
+rcomp=t             Look for reverse-complements of kmers in addition to 
+                    forward kmers.
+maskmiddle=t        (mm) Treat the middle base of a kmer as a wildcard, to 
+                    increase sensitivity in the presence of errors.
+minkmerhits=1       (mkh) Reads need at least this many matching kmers 
+                    to be considered as matching the reference.
+minkmerfraction=0.0 (mkf) A reads needs at least this fraction of its total
+                    kmers to hit a ref, in order to be considered a match.
+                    If this and minkmerhits are set, the greater is used.
+mincovfraction=0.0  (mcf) A reads needs at least this fraction of its total
+                    bases to be covered by ref kmers to be considered a match.
+                    If specified, mcf overrides mkh and mkf.
+hammingdistance=0   (hdist) Maximum Hamming distance for ref kmers (subs only).
+                    Memory use is proportional to (3*K)^hdist.
+qhdist=0            Hamming distance for query kmers; impacts speed, not memory.
+editdistance=0      (edist) Maximum edit distance from ref kmers (subs 
+                    and indels).  Memory use is proportional to (8*K)^edist.
+hammingdistance2=0  (hdist2) Sets hdist for short kmers, when using mink.
+qhdist2=0           Sets qhdist for short kmers, when using mink.
+editdistance2=0     (edist2) Sets edist for short kmers, when using mink.
+forbidn=f           (fn) Forbids matching of read kmers containing N.
+                    By default, these will match a reference 'A' if 
+                    hdist>0 or edist>0, to increase sensitivity.
+removeifeitherbad=t (rieb) Paired reads get sent to 'outmatch' if either is 
+                    match (or either is trimmed shorter than minlen).  
+                    Set to false to require both.
+trimfailures=f      Instead of discarding failed reads, trim them to 1bp.
+                    This makes the statistics a bit odd.
+findbestmatch=f     (fbm) If multiple matches, associate read with sequence 
+                    sharing most kmers.  Reduces speed.
+skipr1=f            Don't do kmer-based operations on read 1.
+skipr2=f            Don't do kmer-based operations on read 2.
+ecco=f              For overlapping paired reads only.  Performs error-
+                    correction with BBMerge prior to kmer operations.
+recalibrate=f       (recal) Recalibrate quality scores.  Requires calibration
+                    matrices generated by CalcTrueQuality.
+sam=<file,file>     If recalibration is desired, and matrices have not already
+                    been generated, BBDuk will create them from the sam file.
+amino=f             Run in amino acid mode.  Some features have not been
+                    tested, but kmer-matching works fine.  Maximum k is 12.
+
+Speed and Memory parameters:
+threads=auto        (t) Set number of threads to use; default is number of 
+                    logical processors.
+prealloc=f          Preallocate memory in table.  Allows faster table loading 
+                    and more efficient memory usage, for a large reference.
+monitor=f           Kill this process if it crashes.  monitor=600,0.01 would 
+                    kill after 600 seconds under 1% usage.
+minrskip=1          (mns) Force minimal skip interval when indexing reference 
+                    kmers.  1 means use all, 2 means use every other kmer, etc.
+maxrskip=1          (mxs) Restrict maximal skip interval when indexing 
+                    reference kmers. Normally all are used for scaffolds<100kb, 
+                    but with longer scaffolds, up to maxrskip-1 are skipped.
+rskip=              Set both minrskip and maxrskip to the same value.
+                    If not set, rskip will vary based on sequence length.
+qskip=1             Skip query kmers to increase speed.  1 means use all.
+speed=0             Ignore this fraction of kmer space (0-15 out of 16) in both
+                    reads and reference.  Increases speed and reduces memory.
+Note: Do not use more than one of 'speed', 'qskip', and 'rskip'.
+
+Trimming/Filtering/Masking parameters:
+Note - if ktrim, kmask, and ksplit are unset, the default behavior is kfilter.
+All kmer processing modes are mutually exclusive.
+Reads only get sent to 'outm' purely based on kmer matches in kfilter mode.
+
+ktrim=f             Trim reads to remove bases matching reference kmers, plus
+                    all bases to the left or right.
+                    Values: 
+                       f (don't trim), 
+                       r (trim to the right), 
+                       l (trim to the left)
+ktrimtips=0         Set this to a positive number to perform ktrim on both
+                    ends, examining only the outermost X bases.
+kmask=              Replace bases matching ref kmers with another symbol.
+                    Allows any non-whitespace character, and processes short
+                    kmers on both ends if mink is set.  'kmask=lc' will
+                    convert masked bases to lowercase.
+maskfullycovered=f  (mfc) Only mask bases that are fully covered by kmers.
+ksplit=f            For single-ended reads only.  Reads will be split into
+                    pairs around the kmer.  If the kmer is at the end of the
+                    read, it will be trimmed instead.  Singletons will go to
+                    out, and pairs will go to outm.  Do not use ksplit with
+                    other operations such as quality-trimming or filtering.
+mink=0              Look for shorter kmers at read tips down to this length, 
+                    when k-trimming or masking.  0 means disabled.  Enabling
+                    this will disable maskmiddle.
+qtrim=f             Trim read ends to remove bases with quality below trimq.
+                    Performed AFTER looking for kmers.  Values: 
+                       rl (trim both ends), 
+                       f (neither end), 
+                       r (right end only), 
+                       l (left end only),
+                       w (sliding window).
+trimq=6             Regions with average quality BELOW this will be trimmed,
+                    if qtrim is set to something other than f.  Can be a 
+                    floating-point number like 7.3.
+trimclip=f          Trim soft-clipped bases from sam files.
+minlength=10        (ml) Reads shorter than this after trimming will be 
+                    discarded.  Pairs will be discarded if both are shorter.
+mlf=0               (minlengthfraction) Reads shorter than this fraction of 
+                    original length after trimming will be discarded.
+maxlength=          Reads longer than this after trimming will be discarded.
+minavgquality=0     (maq) Reads with average quality (after trimming) below 
+                    this will be discarded.
+maqb=0              If positive, calculate maq from this many initial bases.
+minbasequality=0    (mbq) Reads with any base below this quality (after 
+                    trimming) will be discarded.
+maxns=-1            If non-negative, reads with more Ns than this 
+                    (after trimming) will be discarded.
+mcb=0               (minconsecutivebases) Discard reads without at least 
+                    this many consecutive called bases.
+ottm=f              (outputtrimmedtomatch) Output reads trimmed to shorter 
+                    than minlength to outm rather than discarding.
+tp=0                (trimpad) Trim this much extra around matching kmers.
+tbo=f               (trimbyoverlap) Trim adapters based on where paired 
+                    reads overlap.
+strictoverlap=t     Adjust sensitivity for trimbyoverlap mode.
+minoverlap=14       Require this many bases of overlap for detection.
+mininsert=40        Require insert size of at least this for overlap.
+                    Should be reduced to 16 for small RNA sequencing.
+tpe=f               (trimpairsevenly) When kmer right-trimming, trim both 
+                    reads to the minimum length of either.
+forcetrimleft=0     (ftl) If positive, trim bases to the left of this position
+                    (exclusive, 0-based).
+forcetrimright=0    (ftr) If positive, trim bases to the right of this position
+                    (exclusive, 0-based).
+forcetrimright2=0   (ftr2) If positive, trim this many bases on the right end.
+forcetrimmod=0      (ftm) If positive, right-trim length to be equal to zero,
+                    modulo this number.
+restrictleft=0      If positive, only look for kmer matches in the 
+                    leftmost X bases.
+restrictright=0     If positive, only look for kmer matches in the 
+                    rightmost X bases.
+NOTE:  restrictleft and restrictright are mutually exclusive.  If trimming
+       both ends is desired, use ktrimtips.
+mingc=0             Discard reads with GC content below this.
+maxgc=1             Discard reads with GC content above this.
+gcpairs=t           Use average GC of paired reads.
+                    Also affects gchist.
+tossjunk=f          Discard reads with invalid characters as bases.
+swift=f             Trim Swift sequences: Trailing C/T/N R1, leading G/A/N R2.
+
+Header-parsing parameters - these require Illumina headers:
+chastityfilter=f    (cf) Discard reads with id containing ' 1:Y:' or ' 2:Y:'.
+barcodefilter=f     Remove reads with unexpected barcodes if barcodes is set,
+                    or barcodes containing 'N' otherwise.  A barcode must be
+                    the last part of the read header.  Values:
+                       t:     Remove reads with bad barcodes.
+                       f:     Ignore barcodes.
+                       crash: Crash upon encountering bad barcodes.
+barcodes=           Comma-delimited list of barcodes or files of barcodes.
+xmin=-1             If positive, discard reads with a lesser X coordinate.
+ymin=-1             If positive, discard reads with a lesser Y coordinate.
+xmax=-1             If positive, discard reads with a greater X coordinate.
+ymax=-1             If positive, discard reads with a greater Y coordinate.
+
+Polymer trimming:
+trimpolya=0         If greater than 0, trim poly-A or poly-T tails of
+                    at least this length on either end of reads.
+trimpolygleft=0     If greater than 0, trim poly-G prefixes of at least this
+                    length on the left end of reads.  Does not trim poly-C.
+trimpolygright=0    If greater than 0, trim poly-G tails of at least this 
+                    length on the right end of reads.  Does not trim poly-C.
+trimpolyg=0         This sets both left and right at once.
+filterpolyg=0       If greater than 0, remove reads with a poly-G prefix of
+                    at least this length (on the left).
+Note: there are also equivalent poly-C flags.
+
+Polymer tracking:
+pratio=base,base    'pratio=G,C' will print the ratio of G to C polymers.
+plen=20             Length of homopolymers to count.
+
+Entropy/Complexity parameters:
+entropy=-1          Set between 0 and 1 to filter reads with entropy below
+                    that value.  Higher is more stringent.
+entropywindow=50    Calculate entropy using a sliding window of this length.
+entropyk=5          Calculate entropy using kmers of this length.
+minbasefrequency=0  Discard reads with a minimum base frequency below this.
+entropytrim=f       Values:
+                       f:  (false) Do not entropy-trim.
+                       r:  (right) Trim low entropy on the right end only.
+                       l:  (left) Trim low entropy on the left end only.
+                       rl: (both) Trim low entropy on both ends.
+entropymask=f       Values:
+                       f:  (filter) Discard low-entropy sequences.
+                       t:  (true) Mask low-entropy parts of sequences with N.
+                       lc: Change low-entropy parts of sequences to lowercase.
+entropymark=f       Mark each base with its entropy value.  This is on a scale
+                    of 0-41 and is reported as quality scores, so the output
+                    should be fastq or fasta+qual.
+NOTE: If set, entropytrim overrides entropymask.
+
+Cardinality estimation:
+cardinality=f       (loglog) Count unique kmers using the LogLog algorithm.
+cardinalityout=f    (loglogout) Count unique kmers in output reads.
+loglogk=31          Use this kmer length for counting.
+loglogbuckets=2048  Use this many buckets for counting.
+khist=<file>        Kmer frequency histogram; plots number of kmers versus
+                    kmer depth.  This is approximate.
+khistout=<file>     Kmer frequency histogram for output reads.
+
+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
+silent=0
+json=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 1400m 42
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+bbduk() {
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.BBDuk $@"
+	if [[ $silent == 0 ]] && [[ $json == 0 ]]; then
+		echo $CMD >&2
+	fi
+	eval $CMD
+}
+
+bbduk "$@"