--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbcms.sh	Tue Mar 18 17:55:14 2025 -0400
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+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified September 20, 2022
+
+Description:  Error corrects reads and/or filters by depth, storing
+kmer counts in a count-min sketch (a Bloom filter variant).
+This uses a fixed amount of memory.  The error-correction algorithm is taken
+from Tadpole; with plenty of memory, the behavior is almost identical to 
+Tadpole.  As the number of unique kmers in a dataset increases, the accuracy 
+decreases such that it will make fewer corrections.  It is still capable
+of making useful corrections far past the point where Tadpole would crash
+by running out of memory, even with the prefilter flag.  But if there is
+sufficient memory to use Tadpole, then Tadpole is more desirable.
+
+Because accuracy declines with an increasing number of unique kmers, it can
+be useful with very large datasets to run this in 2 passes, with the first 
+pass for filtering only using a 2-bit filter with the flags tossjunk=t and 
+ecc=f (and possibly mincount=2 and hcf=0.4), and the second pass using a 
+4-bit filter for the actual error correction.
+
+Usage:  bbcms.sh in=<input file> out=<output> outb=<reads failing filters>
+
+Example of use in error correction:
+bbcms.sh in=reads.fq out=ecc.fq bits=4 hashes=3 k=31 merge
+
+Example of use in depth filtering:
+bbcms.sh in=reads.fq out=high.fq outb=low.fq k=31 mincount=2 ecc=f hcf=0.4
+
+Error correction and depth filtering can be done simultaneously.
+
+File parameters:
+in=<file>       Primary input, or read 1 input.
+in2=<file>      Read 2 input if reads are in two files.
+out=<file>      Primary read output.
+out2=<file>     Read 2 output if reads are in two files.
+outb=<file>     (outbad/outlow) Output for reads failing mincount.
+outb2=<file>    (outbad2/outlow2) Read 2 output if reads are in two files.
+extra=<file>    Additional comma-delimited files for generating kmer counts.
+ref=<file>      If ref is set, then only files in the ref list will be used
+                for kmer counts, and the input files will NOT be used for
+                counts; they will just be filtered or corrected.
+overwrite=t     (ow) Set to false to force the program to abort rather than
+                overwrite an existing file.
+
+Hashing parameters:
+k=31            Kmer length, currently 1-31.
+hashes=3        Number of hashes per kmer.  Higher generally reduces 
+                false positives at the expense of speed; rapidly
+                diminishing returns above 4.
+ksmall=         Optional sub-kmer length; setting to slightly lower than k 
+                can improve memory efficiency by reducing the number of hashes
+                needed.  e.g. 'k=31 ksmall=29 hashes=2' has better speed and
+                accuracy than 'k=31 hashes=3' when the filter is very full.
+minprob=0.5     Ignore kmers with probability of being correct below this.
+memmult=1.0     Fraction of free memory to use for Bloom filter.  1.0 should
+                generally work; if the program crashes with an out of memory
+                error, set this lower.  You may be able to increase accuracy
+                by setting it slightly higher.
+cells=          Option to set the number of cells manually.  By default this
+                will be autoset to use all available memory.  The only reason
+                to set this is to ensure deterministic output.
+seed=0          This will change the hash function used.  Useful if running
+                iteratively with a very full table.  -1 uses a random seed.
+symmetricwrite=t  (sw) Increases counting accuracy for a slight speed penalty.
+                Could be slow on very low-complexity sequence.
+                
+Depth filtering parameters:
+mincount=0      If positive, reads with kmer counts below mincount will
+                be discarded (sent to outb).
+hcf=1.0         (highcountfraction) Fraction of kmers that must be at least
+                mincount to pass.
+requireboth=t   Require both reads in a pair to pass in order to go to out.
+                When true, if either read has a count below mincount, both
+                reads in the pair will go to outb.  When false, reads will
+                only go to outb if both fail.
+tossjunk=f      Remove reads or pairs with outermost kmer depth below 2.
+(Suggested params for huge metagenomes: mincount=2 hcf=0.4 tossjunk=t)
+
+Error correction parameters:
+ecc=t           Perform error correction.
+bits=           Bits used to store kmer counts; max count is 2^bits-1.
+                Supports 2, 4, 8, 16, or 32.  16 is best for high-depth data;
+                2 or 4 are for huge, low-depth metagenomes that saturate the 
+                bloom filter otherwise.  Generally 4 bits is recommended for 
+                error-correction and 2 bits is recommended for filtering only.
+ecco=f          Error-correct paired reads by overlap prior to kmer-counting.
+merge=t         Merge paired reads by overlap prior to kmer-counting, and 
+                again prior to correction.  Output will still be unmerged.
+smooth=3        Remove spikes from kmer counts due to hash collisions.
+                The number is the max width of peaks to be smoothed; range is
+                0-3 (3 is most aggressive; 0 disables smoothing).
+                This also affects tossjunk.
+                
+
+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/"
+
+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${RAM}m"
+}
+calcXmx "$@"
+
+bloomfilter() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP bloom.BloomFilterCorrectorWrapper $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+bloomfilter "$@"